Production and evaluation of the utility of novel phage display-derived peptide ligands to Salmonella spp. for magnetic separation

Aims: The objectives of this study were to produce Salmonella-specific peptide ligands by phage display biopanning and evaluate their use for magnetic separation (MS).
Methods and Results: Four phage display biopanning rounds were performed and the peptides expressed by the two most Salmonella-specific (on the basis of phage binding ELISA results) phage clones, MSal020401 and MSal020417, were chemically synthesized and coupled to MyOne™ tosylactivated Dynabeads®. Peptide capture capability for whole Salmonella cells from non-enriched broth cultures was quantified by MS + plate counts and MS + Greenlight™ detection, and compared to capture capability of anti-Salmonella (antibody-coated) Dynabeads®. MS + Greenlight™ gave a more comprehensive picture of capture capability than MS + plate counts and showed that Peptide MSal020417-coated beads exhibited at least similar, if not better, capture capability to anti-Salmonella Dynabeads® (mean capture values of 36.0 ± 18.2 % and 31.2 ± 20.1 %, respectively, over Salmonella spp. concentration range 3 x 101 - 3 x 106 cfu ml-1) with minimal cross-reactivity (= 1.9 %) to three other foodborne bacteria.
Conclusions: One of the phage display-derived peptide ligands was demonstrated by MS + Greenlight™ to be a viable antibody-alternative for MS of Salmonella spp.
Significance and Impact of Study: This study demonstrates an antibody-free approach to Salmonella detection and opens substantial possibilities for more rapid tests for this bacterium.

Collectives of diagnostic biomarkers identify high-risk subpopulations of hematuria patients: exploiting heterogeneity in large-scale biomarker data

Background: Ineffective risk stratification can delay diagnosis of serious disease in patients with hematuria. We applied a systems biology approach to analyze clinical, demographic and biomarker measurements (n = 29) collected from 157 hematuric patients: 80 urothelial cancer (UC) and 77 controls with confounding pathologies.

Methods: On the basis of biomarkers, we conducted agglomerative hierarchical clustering to identify patient and biomarker clusters. We then explored the relationship between the patient clusters and clinical characteristics using Chi-square analyses. We determined classification errors and areas under the receiver operating curve of Random Forest Classifiers (RFC) for patient subpopulations using the biomarker clusters to reduce the dimensionality of the data.

Results: Agglomerative clustering identified five patient clusters and seven biomarker clusters. Final diagnoses categories were non-randomly distributed across the five patient clusters. In addition, two of the patient clusters were enriched with patients with ‘low cancer-risk’ characteristics. The biomarkers which contributed to the diagnostic classifiers for these two patient clusters were similar. In contrast, three of the patient clusters were significantly enriched with patients harboring ‘high cancer-risk” characteristics including proteinuria, aggressive pathological stage and grade, and malignant cytology. Patients in these three clusters included controls, that is, patients with other serious disease and patients with cancers other than UC. Biomarkers which contributed to the diagnostic classifiers for the largest ‘high cancer- risk’ cluster were different than those contributing to the classifiers for the ‘low cancer-risk’ clusters. Biomarkers which contributed to subpopulations that were split according to smoking status, gender and medication were different.

Conclusions: The systems biology approach applied in this study allowed the hematuric patients to cluster naturally on the basis of the heterogeneity within their biomarker data, into five distinct risk subpopulations. Our findings highlight an approach with the promise to unlock the potential of biomarkers. This will be especially valuable in the field of diagnostic bladder cancer where biomarkers are urgently required. Clinicians could interpret risk classification scores in the context of clinical parameters at the time of triage. This could reduce cystoscopies and enable priority diagnosis of aggressive diseases, leading to improved patient outcomes at reduced costs. © 2013 Emmert-Streib et al; licensee BioMed Central Ltd.

Identifying trophic variation in a marine suspension feeder:DNA- and stable isotope-based dietary analysis in Mytilus spp.

Accurate field data on trophic interactions for suspension feeders are lacking, and new approaches to dietary analysis are necessary. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was integrated with stable isotope analysis to examine dietary patterns in suspension-feeding Mytilus spp. from seven spatially discrete locations within a semi-enclosed marine bay (Strangford Lough, Northern Ireland) during June 2009. Results of the two methods were highly correlated, reflecting dietary variation in a similar manner. Variation in PCR-DGGE data was more strongly correlated with the principal environmental gradient (distance from the opening to the Irish Sea), while values of dC and dN became progressively enriched, suggesting a greater dependence on animal tissue and benthic microalgae. Diatoms and crustaceans were the most frequently observed phylotypes identified by sequencing, but specific DNA results provided little support for the trophic trends observed in the stable isotope data. This combined approach offers an increased level of trophic insight for suspension feeders and could be applied to other organisms. © 2012 Springer-Verlag Berlin Heidelberg.

Electron paramagnetic resonance studies of nitrogen interstitial defects in diamond

We report on electron paramagnetic resonance (EPR) studies of nitrogen doped diamond that has been N-15 enriched, electron irradiated and annealed. EPR spectra from two new nitrogen containing S = 1/2 defects are detected and labelled WAR9 and WAR10. We show that the properties of these defects are consistent with them being the < 001 >-nitrogen split interstitial and the < 001 >-nitrogen split interstitial-< 001 >-carbon split interstitial pair, respectively. We also provide an explanation for why these defects have previously eluded discovery.

3D deflagration simulations leaving bound remnants:A model for 2002cx-like Type Ia supernovae

2002cx-like supernovae are a sub-class of sub-luminous Type Ia supernovae (SNe). Their light curves and spectra are characterized by distinct features that indicate strong mixing of the explosion ejecta. Pure turbulent deflagrations have been shown to produce such mixed ejecta. Here, we present hydrodynamics, nucleosynthesis and radiative-transfer calculations for a 3D full-star deflagration of a Chandrasekhar-mass white dwarf. Our model is able to reproduce the characteristic observational features of SN 2005hk (a prototypical 2002cx-like supernova), not only in the optical, but also in the near-infrared. For that purpose we present, for the first time, five near-infrared spectra of SN 2005hk from -0.2 to 26.6 d with respect to B-band maximum. Since our model burns only small parts of the initial white dwarf, it fails to completely unbind the white dwarf and leaves behind a bound remnant of ~1.03Mconsisting mainly of unburned carbon and oxygen, but also enriched by some amount of intermediate-mass and iron-group elements from the explosion products that fall back on the remnant.We discuss possibilities for detecting this bound remnant and how it might influence the late-time observables of 2002cx-like SNe. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.

Inclusion & the Special Educational Needs (SEN) Resource Base In Mainstream Schools: Physical Factors to Maximise Effectiveness.

As a society, we have a responsibility to provide an inclusive built environment. As part of the need to promote inclusion, there is now a growing trend to place pupils with Special Educational Needs (SEN) into a mainstream school setting. This is often facilitated by providing a specialist SEN resource base located within the mainstream school. If so, the following paper outlines why the whole school should be considered when locating and implementing a SEN resource base. It also highlights the wider opportunities for enhancing inclusion for SEN pupils if giving holistic thought to the wider context of the resource base. It then indicates a four-stage approach, using the ASD pupil as an illustrative example, to help evaluate the optimum SEN resource base location within a mainstream school setting. Finally it highlights in conclusion, some benefits and challenges for an enriched school environment for all pupils, if considering genuine inclusion.

Interstitial Nitrogen in Diamond – Optical and EPR Studies

Nitrogen is one of the most common impurities in diamond. On a substitutional site it acts as a deep donor, approximately 1.7 eV below the conduction band. Irradiation of nitrogen containing diamond and subsequent annealing creates the nitrogen vacancy centre, which has recently attracted much attention for quantum information processing application. Another possible product of irradiation and annealing of nitrogen containing diamond is interstitial nitrogen. Presumably, a mobile carbon interstitial migrates to a substitutional nitrogen to produce an interstitial nitrogen complex which may or may not be mobile. The configuration(s) of interstitial nitrogen related defects (e.g. bond centred, [001]-split) are not known. An infra-red (IR) absorption peak at 1450 cm-1 labelled H1a has been associated with an nitrogen interstitial complex. [1] Theoretical modelling suggested that this IR local mode is due to a bond centred nitrogen interstitial [2]. However, more recent modelling [3] suggests that this defect is mobile at temperatures were H1a is stable and instead assign H1a to two nitrogen atoms occupying a single lattice site in a [001]-split configuration. To date no electron paramagnetic resonance (EPR) spectra have been conclusively associated with an interstitial nitrogen defect.

In this study we present data from new EPR and optical absorption studies in combination with uniaxial stress of nitrogen interstitial related defects in electron irradiated and annealed nitrogen doped diamond. These measurements yield symmetry information about the defects allowing us to determine which of the proposed models are possible. EPR spectra of nitrogen interstitial related defects in samples isotopically enriched with 15N are reported and we show that these explain the lack of previous EPR data for these defects. Correlations between the IR absorbance and the integrated intensity of the new EPR defects are studied for varying irradiation doses and annealing temperatures.

Catalytic conversion of sodium lignosulphonate to vanillin –engineering aspects. Part 1 Effect of processing conditionson vanillin yield and selectivity

The commercial production of vanillin from sodium lignosulfonate under highly alkaline conditions, catalyzed by Cu2+ at elevated temperature and pressures up to 10 bar, has been simulated in a 3-L stirred reactor. Initially, the process was operated in the presence of nitrogen in dead-end mode, and it was shown that vanillin and vanillic acid were formed by hydrolysis at temperatures of 120, 140, and 160 °C. At the two higher temperatures, the amount of vanillin produced was the same. Subsequently, experiments were conducted at the same elevated pressures and temperatures with addition of air or oxygen-enriched air once the temperature in the reactor had reached temperatures similar to those used when only hydrolysis occurred. In this case, the concentration of vanillin at 140 and 160 °C was equal to that due to hydrolysis, and the subsequent 2-fold increase was due to oxidation. In addition, both vanillic acid and acetovanillone (which has rarely been reported) were produced, as was hydrogen. Thus, for the first time, it has been shown that the production of vanillin (and other compounds) from sodium lignosulfonate at elevated temperatures involves hydrolysis and oxidation, with hydrolysis starting at just above 100 °C, that is, much lower than has previously been reported. Approximately 50% is produced by each mechanism. In addition, the orders of the reactions of the different steps were estimated, and the reaction mechanisms are discussed.

Shifting Ground:Beyond National Architecture

The Irish Pavilion at the Venice Architecture Biennale 2012 charts a position for Irish architecture in a global culture where the modes of production of architecture are radically altered. Ireland is one of the most globalised countries in the world, yet it has developed a national culture of architecture derived from local place as a material construct. We now have to evolve our understanding in the light of the globalised nature of economic processes and architectural production which is largely dependent on internationally networked flows of products, data, and knowledge. We have just begun to represent this situation to ourselves and others. How should a global architecture be grounded culturally and philosophically? How does it position itself outside of shared national reference points?
heneghan peng architects were selected as participants because they are working across three continents on a range of competition-winning projects. Several of these are in sensitive and/or symbolic sites that include three UNESCO World Heritage sites, including the Grand Egyptian Museum in Cairo, the Giants Causeway Visitor Centre in Northern Ireland, and the new Rhine Bridge near Lorelei.
Our dialogue led us to discussing the universal languages of projective geometry and number are been shared by architects and related professionals. In the work of heneghan peng, the specific embodiment of these geometries is carefully calibrated by the choice of materials and the detailed design of their physical performance on site. The stone facade of the Giant’s Causeway Visitor Centre takes precise measure of the properties of the volcanic basalt seams from which it is hewn. The extraction of the stone is the subject of the pavilion wall drawings which record the cutting of stones to create the façade of the causeway centre.
We also identified water as an element which is shared across the different sites. Venice is a perfect place to take measure of this element which suggests links to another site – the Nile Valley which was enriched by the annual flooding of the River Nile. An ancient Egyptian rod for measuring the water level of the Nile inspired the design of the Nilometre - a responsive oscillating bench that invites visitors to balance their respective weights. This action embodies the ways of thinking that are evolving to operate in the globalised world, where the autonomous architectural object is dissolving into an expanded field of conceptual rules and systems. The bench constitutes a shifting ground located in the unstable field of Venice. It is about measurement and calibration of the weight of the body in relation to other bodies; in relation to the site of the installation; and in relation to water. The exhibit is located in the Artiglierie section of the Arsenale. Its level is calibrated against the mark of the acqua alta in the adjacent brickwork of the building which embodies a liminal moment in the fluctuating level of the lagoon.
The weights of bodies, the level of water, changes over time, are constant aspects of design across cultures and collectively they constitute a common ground for architecture - a ground shared with other design professionals. The movement of the bench required complex engineering design and active collaboration between the architects, engineers and fabricators. It is a kind of prototype – a physical object produced from digital data that explores the mathematics at play – the see-saw motion invites the observer to become a participant, to give it a test drive. It shows how a simple principle can generate complex effects that are difficult to predict and invites visitors to experiment and play with them.

Phosphorylation of plant actin-depolymerising factor by calmodulin-like domain protein kinase

actin-depolymerising factor (ADF)/cofilin group of proteins are stimulus-responsive actin-severing proteins, members of which are regulated by reversible phosphorylation. The phosphorylation site on the maize ADF, ZmADF3, is Ser-6 but the kinase responsible is unknown [Smertenko et al,, Plant J. 14 (1998) 187-193]. We have partially purified the ADF kinase(s) and found it to be calcium-regulated and inhibited by N-(6-aminohesyl)-[H-3]5-chloro-1-naphthalenesulphonamide. Immunoblotting reveals that calmodulin-like domain protein kinase(s) (CDPK) are enriched in the purified preparation and addition of anti-CDPK to in vitro phosphorylation assays results in the inhibition of ADF phosphorylation, These data strongly suggest that plant ADP is phosphorylation by CDPK(s), a class of protein kinases unique to plants and protozoa. (C) 2001 Published by Elsevier Science B.V. on behalf of the Federation of European Biochemical Societies.

Differences in Mucosal Gene Expression in the Colon of Two Inbred Mouse Strains after Colonization with Commensal Gut Bacteria

The host genotype has been proposed to contribute to individually composed bacterial communities in the gut. To provide deeper insight into interactions between gut bacteria and host, we associated germ-free C3H and C57BL/10 mice with intestinal bacteria from a C57BL/10 donor mouse. Analysis of microbiota similarity between the animals with denaturing gradient gel electrophoresis revealed the development of a mouse strain-specific microbiota. Microarray-based gene expression analysis in the colonic mucosa identified 202 genes whose expression differed significantly by a factor of more than 2. Application of bioinformatics tools demonstrated that functional terms including signaling/secretion, lipid degradation/catabolism, guanine nucleotide/guanylate binding and immune response were significantly enriched in differentially expressed genes. We had a closer look at the 56 genes with expression differences of more than 4 and observed a higher expression in C57BL/10 mice of the genes coding for Tlr1 and Ang4 which are involved in the recognition and response to gut bacteria. A higher expression of Pla2g2a was detected in C3H mice. In addition, a number of interferon-inducible genes were higher expressed in C3H than in C57BL/10 mice including Gbp1, Mal, Oasl2, Ifi202b, Rtp4, Ly6g6c, Ifi27l2a, Usp18, Ifit1, Ifi44, and Ly6g indicating that interferons may play an essential role in microbiota regulation. However, genes coding for interferons, their receptors, factors involved in interferon expression regulation or signaling pathways were not differentially expressed between the two mouse strains. Taken together, our study confirms that the host genotype is involved in the establishment of host-specific bacterial communities in the gut. Based on expression differences after colonization with the same bacterial inoculum, we propose that Pla2g2a and interferon-dependent genes may contribute to this phenomenon.

Impact of a play-based curriculum in the first two years of primary school: literacy and numeracy outcomes over seven years

In 2000–2002 an innovative early years curriculum, the Enriched Curriculum (EC), was introduced
into 120 volunteer schools across Northern Ireland, replacing a traditional curriculum similar to
others across the UK at that time. It was intended by the designers to be developmentally appropriate
and play-based with the primary goal of preventing the experience of persistent early failure in
children. The EC was not intended to be a literacy and numeracy intervention, yet it did considerably
alter pedagogy in these domains, particularly the age at which formal reading and mathematics
instruction began. As part of a multi-method evaluation running from 2000–2008, the research
team followed the primary school careers of the first two successive cohorts of EC children, comparing
them with year-ahead controls attending the same 24 schools. Compared to the year-ahead control
group, the findings show that the EC children’s reading and mathematics scores fell behind in
the first two years but the majority of EC children caught up by the end of their fourth year. Thereafter,
the performance of the first EC cohort fell away slightly, while that of the second continued to
match that of controls. Overall, the play-based curriculum had no statistically significant positive
effects on reading and mathematics in the medium term. At best, the EC children’s scores matched
those of controls.

Strudel: A corpus-based semantic model based on properties and types

Computational models of meaning trained on naturally occurring text successfully model human performance on tasks involving simple similarity measures, but they characterize meaning in terms of undifferentiated bags of words or topical dimensions. This has led some to question their psychological plausibility (Murphy, 2002; Schunn, 1999). We present here a fully automatic method for extracting a structured and comprehensive set of concept descriptions directly from an English part-of-speech-tagged corpus. Concepts are characterized by weighted properties, enriched with concept-property types that approximate classical relations such as hypernymy and function. Our model outperforms comparable algorithms in cognitive tasks pertaining not only to concept-internal structures (discovering properties of concepts, grouping properties by property type) but also to inter-concept relations (clustering into superordinates), suggesting the empirical validity of the property-based approach. Copyright © 2009 Cognitive Science Society, Inc. All rights reserved.

Preparation of planar retinal specimens:verification by histology, mRNA profiling, and proteome analysis

Elucidation of the transcriptome and proteome of the normal retina will be difficult since it is comprised of at least 55 different cell types. However the characteristic layered cellular anatomy of the retina makes it amenable to planar sectioning, enabling the generation of enriched retinal cell populations. The aim of this study was to validate a reproducible method for preparing enriched retinal layers from porcine retina.

Ion-acoustic supersolitons in plasmas with two-temperature electrons: Boltzmann and kappa distributions

Acoustic supersolitons arise when a plasma model is able to support three consecutive local extrema of the Sagdeev pseudopotential between the undisturbed conditions and an accessible root. This leads to a characteristic electric field signature, where a simple bipolar shape is enriched by subsidiary maxima. Large-amplitude nonlinear acoustic modes are investigated, using a pseudopotential approach, for plasmas containing two-temperature electrons having Boltzmann or kappa distributions, in the presence of cold fluid ions. The existence domains for positive supersolitons are derived in a methodological way, both for structure velocities and amplitudes, in terms of plasma compositional parameters. In addition, typical pseudopotentials, soliton, and electric field profiles have been given to illustrate that positive supersolitons can be found in the whole range of electron distributions from Maxwellian to a very hard nonthermal spectrum in kappa. However, it is found that the parameter ranges that support supersolitons vary significantly over the wide range of kappa considered. VC 2013 AIP Publishing LLC. [http://dx.doi.org/10.1063/1.4818888]