Growth of Gold Nanocrystals Incorporated with Magnetic Microbead-based Separation as a Tool for Quantification of Biological Interactions

Au nanoparticles (AuNPs) have been widely used not only as optical labels or ‘weight” labels for the detections of biorecognition events but also an amplifier of surface plasmon resonance biosensors. The intrinsic property of gold nuclei composing of a group of Au atoms to catalyze the reduction of metal ions on the NPs and thereby to enlarge the metallic nanoparticles is employed in different biosensing paths. In a solution containing Au+ ions (e.g. HAuCl4) and the Au clusters, hydrated electrons which are reduced from oxidation of reducers (H2O2, sodium citrate, ascorbic acid, or NaBH4) will be used to reduce the Au+ ion leading to the deposition of Au+ to the Au0 (Au clusters). The reaction will be catalyzed continuously by the Au0 until the Au+ ions and hydrated electrons are exhausted. As a result, the AuNPs will be grown and their optical properties are also changed. If the AuNP nanoclusters are used as probes, the color change will be dependent on amount of analytes, thus give a quantitative monitoring of the analytes.

In this study, we incorporate the use of magnetic beads with the nanocrystalline growth to quantify a target protein based on immunoreactions. Prostate specific antigen (PSA) is chosen as the target analyte because of its values in diagnosis of prostate cancer. A double-sandwiched immunoassay is performed by gold-tagged monoclonal PSA antibody-PSA antigen – magnetic bead-tagged polyclonal PSA antibody interactions. After the immunoreactions, the target analytes are preconcentrated and separated by the magnetic beads while the nanogrowth plays a role of colorimetric signal developer.

The result shows that this is a very sensitive, robust and excellent strategy to detect biological interactions. PSA antigen is detected at femtomolar level with very high specificity under the presence of undesired proteins of crude samples. Furthermore, the method also shows great potential to detect other biological interactions. More details will be described in our presentation.

Deriving the Edge: What's in a phase?

This article offers a critical conceptual discussion and refinement of Chomsky’s (2000, 2001, 2007, 2008) phase system, addressing many of the problematic aspects highlighted in the critique of Boeckx & Grohmann (2007) and seeking to resolve these issues, in particular the stipulative and arbitrary properties of phases and phase edges encoded in the (various versions of the) Phase Impenetrability Condition (PIC). Chomsky’s (2000) original conception of phases as lexical subarrays is demonstrated to derive these properties straightforwardly once a single assumption about the pairwise composition of phases is made, and the PIC is reduced to its necessary core under the Strong Minimalist Thesis (SMT)—namely, the provision of an edge. Finally, a comparison is undertaken of the lexical-subarray conception of phases with the feature-inheritance system of Chomsky 2007, 2008, in which phases are simply the locus of uninterpretable features (probes). Both conceptions are argued to conform to the SMT, and both converge on a pairwise composition of phases. However, the two conceptions of phases are argued to be mutually incompatible in numerous fundamental ways, with no current prospect of unification. The lexical-subarray conception of phases is then to be preferred on grounds of greater empirical adequacy.

Violence and social memory in twentieth century Belfast:Stories of Buck Alec Robinson

This article explores the life and commemoration of Buck Alec Robinson. A feared loyalist killer in 1920s Belfast, in more recent times he has featured as a lion-keeping “character” on wall murals and in tourist guide books. Robinson is employed as a case study to investigate two separate but, in this case, interlinked historiographical debates. The first involves Norbert Elias’s analysis of the decline of violence. The second relates to discussion of the analysis of social memory in working class communities, with violence being placed therein. The article supports historical assessments suggesting that the “civilizing offensive” had an uneven impact. That point is usually made in the context of working class men. This article extends it to political elites in Belfast and probes their flirtations with violent hard men. The case is made that it is a mistake to assume the “civilizing” dynamic is to be understood as a teleological or top-down process.

A PCR-based method to distinguish fungi of the rice sheath-blight complex, Rhizoctonia solani, R. oryzae and R. oryzae-sativae

Identification of Rhizoctonia solani, R. oryzae and R. oryzae-sativae, components of the rice sheath disease complex, is extremely difficult and often inaccurate and as a result may hinder the success of extensive breeding programmes throughout Asia. In this study, primers designed from unique regions within the rDNA internal transcribed spacers have been used to develop a rapid PCR-based diagnostic test to provide an accurate identification of the species on rice. Tests on the specificity of the primers concerned showed that they provide the means for accurate identification of the Rhizoctonia species responsible for sheath diseases in rice.

Discharge kinetics of inductively coupled oxygen plasmas:Experiment and model

In this paper, neutral and charged particle dynamics in both the capacitive and inductive modes of an inductively coupled oxygen discharge are presented. Langmuir probes, laser-assisted photodetachment and two-photon laser-induced fluorescence are employed to measure plasma parameters in the 13.56MHz system for a range of plasma powers and gas pressures. It is found that the capacitive mode is more electronegative with lower molecular dissociation compared with the inductive mode. However, the negative ion density in each mode is comparable. A maximum is observed in the negative ion density and fraction with pressure for both modes. The experimental measurements are supplemented by a global model, which includes capacitive and inductive coupling effects. The model and experiments demonstrate that negative ion loss is dominated by ion-ion recombination and electron detachment at low pressures (

Truth Recovery and Transitional Justice: Deferring human rights issues

This book investigates why some societies defer the solution of transitional justice issues, such as the disappeared/missing, even after successful democratic consolidation. It also explains why the same societies finally decide to deal with these human rights issues. In short, it considers the interesting and understudied phenomenon of post-transitional justice. The prolonged silences in Spain, Cyprus and Greece contradict the experience of other countries -- such as South Africa, Bosnia, and Guatemala -- where truth recovery for disappeared/missing persons was a central element of the transition to peace and democracy. Despite democratization, the exhumation of mass graves containing the victims from the violence in Cyprus (1963-1974) and the Spanish civil war (1936-1939) was delayed until the early 2000s, when both countries suddenly decided to revisit the past. Cyprus and Spain are not alone: this is an increasing trend among countries trying to come to terms with past violence. Interestingly, despite similar background conditions, Greece is resisting the trend, challenging both theory and regional experience. Truth Recovery and Transitional Justice considers three interrelated issues. First, what factors can explain prolonged silence on the issue of missing persons in some transitional settings? Second, which processes can address the occasional yet puzzling transformation of victims’ groups from opponents of truth recovery to vocal pro-reconciliation pressure groups? Third, under which conditions is it better to tie victims’ rights to an overall political settlement? The book looks at Spain and Cyprus to show how they have attempted to bring closure to deep trauma by exhuming and identifying their missing, albeit under considerably different conditions. It then probes the generalizability of the conclusions on Spain and Cyprus by looking at the Greek experience; oddly, despite similar background conditions, Greece remains resistant to post-transitional justice norms. Interestingly, each case study takes a different approach to transitional justice.

Scanning Probe Microscopy for Energy Research : Materials, Devices, and Applications:Scanning Probe Microscopy for Energy Research : Materials, Devices, and Applications

Scanning Probes for Fuel Cells and Local Electrochemistry

Linking watershed terrain and hydrology to soil chemical properties, microbial communities and impacts on soil organic C in a humid mid-latitude forested watershed

Understanding the response of humid mid-latitude forests to changes in precipitation, temperature, nutrient cycling, and disturbance is critical to improving our predictive understanding of changes in the surface-subsurface energy balance due to climate change. Mechanistic understanding of the effects of long-term and transient moisture conditions are needed to quantify
linkages between changing redox conditions, microbial activity, and soil mineral and nutrient interactions on C cycling and greenhouse gas releases. To illuminate relationships between the soil chemistry, microbial communities and organic C we established transects across hydraulic and topographic gradients in a small watershed with transient moisture conditions. Valley bottoms tend to be more frequently saturated than ridge tops and side slopes which generally are only saturated when shallow storm flow zones are active. Fifty shallow (~36”) soil cores were collected during timeframes representative of low CO2, soil winter conditions and high CO2, soil summer conditions. Cores were subdivided into 240 samples based on pedology and analyses of the geochemical (moisture content, metals, pH, Fe species, N, C, CEC, AEC) and microbial (16S rRNA gene
amplification with Illumina MiSeq sequencing) characteristics were conducted and correlated to watershed terrain and hydrology. To associate microbial metabolic activity with greenhouse gas emissions we installed 17 soil gas probes, collected gas samples for 16 months and analyzed them for CO2 and other fixed and greenhouse gasses. Parallel to the experimental efforts our data is being used to support hydrobiogeochemical process modeling by coupling the Community Land Model (CLM) with a subsurface process model (PFLOTRAN) to simulate processes and interactions from the molecular to watershed scales. Including above ground processes (biogeophysics, hydrology, and vegetation dynamics), CLM provides mechanistic water, energy, and organic matter inputs to the surface/subsurface models, in which coupled biogeochemical reaction
networks are used to improve the representation of below-ground processes. Preliminary results suggest that inclusion of above ground processes from CLM greatly improves the prediction of moisture response and water cycle at the watershed scale.

Epstein-Barr Virus Large Tegument Protein BPLF1 Contributes to Innate Immune Evasion through Interference with Toll-Like Receptor Signaling

Viral infection triggers an early host response through activation of pattern recognition receptors, including Toll-like receptors (TLR). TLR signaling cascades induce production of type I interferons and proinflammatory cytokines involved in establishing an anti-viral state as well as in orchestrating ensuing adaptive immunity. To allow infection, replication, and persistence, (herpes)viruses employ ingenious strategies to evade host immunity. The human gamma-herpesvirus Epstein-Barr virus (EBV) is a large, enveloped DNA virus persistently carried by more than 90% of adults worldwide. It is the causative agent of infectious mononucleosis and is associated with several malignant tumors. EBV activates TLRs, including TLR2, TLR3, and TLR9. Interestingly, both the expression of and signaling by TLRs is attenuated during productive EBV infection. Ubiquitination plays an important role in regulating TLR signaling and is controlled by ubiquitin ligases and deubiquitinases (DUBs). The EBV genome encodes three proteins reported to exert in vitro deubiquitinase activity. Using active site-directed probes, we show that one of these putative DUBs, the conserved herpesvirus large tegument protein BPLF1, acts as a functional DUB in EBV-producing B cells. The BPLF1 enzyme is expressed during the late phase of lytic EBV infection and is incorporated into viral particles. The N-terminal part of the large BPLF1 protein contains the catalytic site for DUB activity and suppresses TLR-mediated activation of NF-κB at, or downstream of, the TRAF6 signaling intermediate. A catalytically inactive mutant of this EBV protein did not reduce NF-κB activation, indicating that DUB activity is essential for attenuating TLR signal transduction. Our combined results show that EBV employs deubiquitination of signaling intermediates in the TLR cascade as a mechanism to counteract innate anti-viral immunity of infected hosts.

Ionic liquids for efficient hydrogen sulfide and thiol scavenging

Functionalised pyridinium and ammonium ionic liquids bearing a Michael acceptor are shown to scavenge H₂S gas and various thiols, in most cases, without the aid of any added bases. Utilising the effective non-volatility of ionic liquids and ‘tagging’ malodourous substances to an ionic matrix renders them odourless.

Religion, Violence and Cities

In exploring the connections between religion, violence and cities, the book probes the extent to which religion moderates or exacerbates violence in an increasingly urbanised world. Originating in a five year research project , Conflict in Cities and the Contested State, concerned with Belfast, Jerusalem and other ethno-nationally divided cities, this volume widens the geographical focus to include diverse cities from the Balkans, the Middle East, Nigeria and Japan. In addressing the understudied triangular relationships between religion, violence and cities, contributors stress the multiple forms taken by religion and violence while challenging the compartmentalisation of two highly topical debates – links between religion and violence on the one hand, and the proliferation of violent urban conflicts on the other hand. Their research demonstrates why cities have become so important in conflicts driven by state-building, fundamentalism, religious nationalism, and ethno-religious division and illuminates the conditions under which urban environments can fuel violent conflicts while simultaneously providing opportunities for managing or transforming them.

COD and NH4-N Estimation in the Inflow of Wastewater Treatment Plants using Machine Learning Techniques

The in-line measurement of COD and NH4-N in the WWTP inflow is crucial for the timely monitoring of biological wastewater treatment processes and for the development of advanced control strategies for optimized WWTP operation. As a direct measurement of COD and NH4-N requires expensive and high maintenance in-line probes or analyzers, an approach estimating COD and NH4-N based on standard and spectroscopic in-line inflow measurement systems using Machine Learning Techniques is presented in this paper. The results show that COD estimation using Radom Forest Regression with a normalized MSE of 0.3, which is sufficiently accurate for practical applications, can be achieved using only standard in-line measurements. In the case of NH4-N, a good estimation using Partial Least Squares Regression with a normalized MSE of 0.16 is only possible based on a combination of standard and spectroscopic in-line measurements. Furthermore, the comparison of regression and classification methods shows that both methods perform equally well in most cases.

Targeting Trypsin-Like Proteases: A Mechanism to Restore Mucociliary Function in Cystic Fibrosis Airways

Dehydration of the airway surface liquid (ASL) and the resultant decline in function of the mucociliary escalator in cystic fibrosis airways is largely underpinned by the excessive flux of Na+ and water though ENaC. Proteolysis of the endogenous  and  subunits of epithelial sodium channels (ENaC) by channel activating proteases (CAPS) is the key regulatory mechanism for channel activation. Recent reports highlight that (1) CFTR (cystic fibrosis transmembrane conductance regulator) normally protects ENaC from the action of proteases and (2) a stark imbalance in proteases/protease inhibitor levels in CF airway cultures favour activation of normally inactive ENaC. The current study examines the potential therapeutic benefit of CAPS/ENaC inhibition in CF airways.
Our group has developed a panel of active-site directed affinity-based probes which target and inhibit trypsin-like proteases (potential CAPS); including the broad-spectrum inhibitor QUB-TL1. We have utilised this compound to interrogate the impact of trypsin-like protease inhibition on ENaC activity in differentiated primary airway epithelial cell cultures.
Electrophysiological data demonstrate QUB-TL1 selectively and irreversibly binds to extracellularly located trypsin-like proteases resulting in impaired ENaC-mediated Na+ transport. Visualisation of ENaC at the apical surface compartment of primary airway epithelial cells shows a large reduction in a low molecular weight (processed and active) form of ENaC, which was found to be abundant in untreated CF cultures. Consistent with the reduction in ENaC activity observed, QUB-TL1 treatment was subsequently shown to increase ASL height (performed in collaboration with Royal College of Surgeons in Ireland).
Our results are consistent with the hypothesis that targeting the CAPS-ENaC signalling axis may restore the depleted ASL seen in CF airways.

Distinct methylation patterns in genes that affect mitochondrial function are associated with kidney disease in blood-derived DNA from individuals with Type 1 diabetes

AIMS: Epigenetic modifications, such as DNA methylation, can influence the risk of developing kidney disease. We studied methylation profiles in genes related to mitochondrial function to assess whether differences in these epigenetic features were associated with diabetic kidney disease in people with Type 1 diabetes.

METHODS: A case-control association study was undertaken (n = 196 individuals with diabetic kidney disease vs. n = 246 individuals without renal disease). Participants were White and diagnosed with Type 1 diabetes before 31 years of age. Genes that encode mitochondrial proteins (n = 780) were downloaded from mitoproteome. org. DNA methylation profiles from blood-derived DNA were generated using the Illumina Infinium HumanMethylation450 (262 samples) and Illumina Infinium HumanMethylation27 (192 samples) arrays. Beta values (β) were calculated and quality control was conducted, including evaluating blind duplicate DNA samples.

RESULTS: Fifty-four Cytosine-phosphate-Guanine probes across 51 unique genes were significantly associated (P ≤ 10(-8) ) with diabetic kidney disease across both the 450K and the 27K methylation arrays. A subanalysis, employing the 450K array, identified 755 Cytosine-phosphate-Guanine probes in 374 genes that were significantly associated (P ≤ 10(-8) ) with end-stage renal disease. Forty-six of the top-ranked variants for diabetic kidney disease were also identified as being differentially methylated in individuals with end-stage renal disease. The largest change in methylation (Δβ = 0.2) was observed for cg03169527 in the TAMM41 gene, chromosome 3p25.2. Three genes, PMPCB, TSFM and AUH, were observed with differential methylation at multiple Cytosine-phosphate-Guanine sites each (P < 10(-12) ).

CONCLUSIONS: Differential methylation in genes that influence mitochondrial function are associated with kidney disease in individuals with Type 1 diabetes. 

New insights into sequence variation in the IGS region of 21 cyathostomin species and the implication for molecular identification

Cyathostomins comprise a group of 50 species of parasitic nematodes that infect equids. Ribosomal DNA sequences, in particular the intergenic spacer (IGS) region, have been utilized via several methodologies to identify pre-parasitic stages of the commonest species that affect horses. These methods rely on the availability of accurate sequence information for each species, as well as detailed knowledge of the levels of intra- and inter-specific variation. Here, the IGS DNA region was amplified and sequenced from 10 cyathostomin species for which sequence was not previously available. Also, additional IGS DNA sequences were generated from individual worms of 8 species already studied. Comparative analysis of these sequences revealed a greater range of intra-specific variation than previously reported (up to 23%); whilst the level of inter-specific variation (3-62%) was similar to that identified in earlier studies. The reverse line blot (RLB) method has been used to exploit the cyathostomin IGS DNA region for species identification. Here, we report validation of novel and existing DNA probes for identification of cyathostomins using this method and highlight their application in differentiating life-cycle stages such as third-stage larvae that cannot be identified to species by morphological means.