An antibody-lectin sandwich assay for quantifying protein glycoforms.

We describe an antibody-lectin sandwich assay for quantitation of glycoforms of proteins. The assay uses deglycosylated IgG antibody immobilized on a microtiter plate to capture the protein of interest from the sample. The particular glycoform is then identified by reaction with biotin-labeled lectin, which is measured using streptavidin/alkaline phosphatase. The assay can be adapted to quantitate any protein’s glycoforms by simply substituting the antibody and lectin with specific alternatives,

Quantifying, characterizing, and controlling information flow in ultracold atomic gases

We study quantum information flow in a model comprised of a trapped impurity qubit immersed in a Bose-Einstein-condensed reservoir. We demonstrate how information flux between the qubit and the condensate can be manipulated by engineering the ultracold reservoir within experimentally realistic limits. We show that this system undergoes a transition from Markovian to non-Markovian dynamics, which can be controlled by changing key parameters such as the condensate scattering length. In this way, one can realize a quantum simulator of both Markovian and non-Markovian open quantum systems, the latter ones being characterized by a reverse flow of information from the background gas (reservoir) to the impurity (system).

Quantifying the Energy & carbon emissions implications of a 10% electric vehicles target

EU Directive 2009/28/EC on Renewable Energy requires each Member State to ensure 10% of transport energy (excluding aviation and marine transport) comes from renewable sources by 2020 (10% RES-T target). In addition to the anticipated growth in biofuels, this target is expected to be met by the increased electrification of transport coupled with a growing contribution from renewable energy to electricity generation. Energy use in transport accounted for nearly half of Ireland’s total final energy demand and about a third of energy-related carbon dioxide emissions in 2007. Energy use in transport has grown by 6.3% per annum on average in the period 1990 – 2007. This high share and fast growth relative to other countries highlights the challenges Ireland faces in meeting ambitious renewable energy targets. The Irish Government has set a specific target for Electric Vehicles (EV) as part of its strategy to deliver the 10% RES-T target. By 2020, 10% of all vehicles in its transport fleet are to be powered by electricity. This paper quantifies the impacts on energy and carbon dioxide emissions of this 10% EV target by 2020. In order to do this an ‘EV Car Stock’ model was developed to analyse the historical and future make-up of the passenger car portion of the fleet to 2025. Three scenarios for possible take-up in EVs were examined and the associated energy and emissions impacts are quantified. These impacts are then compared to Ireland’s 10% RES-T target and greenhouse gas (GHG) emissions reduction targets for 2020. Two key findings of the study are that the 10% EV target contributes 1.7% to the 10% RES-T target by 2020 and 1.4% to the 20% reduction in Non-ETS emissions by 2020 relative to 2005.

Quantifying contributions of domestic wastewater treatment systems to nutrient fluxes in stream headwaters

Effective implementation of the Water Framework Directive requires a reappraisal of conventional approaches to water quality monitoring. Quantifying the impact of domestic wastewater treatment systems (DWWTS) in Irish catchments is further complicated by high levels of natural heterogeneity. This paper presents a numerical model that couples attenuation to flow along different hydrological pathways contributing to river discharge; this permits estimation of the impact of DWWTS to overall nutrient fluxes under a range of geological conditions. Preliminary results suggest high levels of attenuation experienced
before DWWTS effluent reaches bedrock play a significant role in reducing its ecological impact on aquatic receptors. Conversely, low levels of attenuation in systems discharging directly to surface water may affect water quality more significantly, particularly during prolonged dry periods in areas underlain by low productivity aquifers (>60% of Ireland), where dilution capacity is limited.

Quantifying mircoorganism/organic matter interactions in saturated porous media.

Proteins and humic acids are common constituents of waste water. Latex colloids (colloids) acted as surrogates for microorganisms in multiple pulse dynamic column experiments (MPEs) that permitted colloid mobility to be quantified before and after the injection of either BSA (a protein), or Suwannee River humic acid (SRHA).
At low OM coverage colloid breakthrough curves demonstrated both BSA and SRHA reduced colloid deposition rates, but did not affect colloid irreversible deposition mechanisms. By contrast, high levels of SRHA surface coverage not only further reduced the matrix’s ability to attenuate colloids, but also resulted in reversible adsorption of a significant fraction of colloids deposited. Modelling of colloid responses using random sequential adsorption modelling suggested that 1 microgram of SRHA had the same effect as the deposition of 5.90±0.14 x109 colloids; the model suggested that adsorption of the same mass of BSA was equivalent to the deposition of between 7.1x108 and 2.3x109 colloids.
Colloid responses in MPEs where BSA coverage of colloid deposition sites approached saturation demonstrated the sand matrix remained capable of adsorbing colloids. However, in contrast to responses observed in MPEs at low surface coverage, continued colloid injection showed that the sand’s attenuation capacity increased with time, i.e. colloid concentrations declined as more were deposited (filter ripening).
Importance: Study results highlight the contrasting responses that may arise due to the interactions between colloids and OM in porous media. Results not only underscore that colloids can interact differently with various forms of deposited OM, but also that a single type of OM may generate dramatically different responses depending on the degree of surface coverage. The MPE method provides a means of quantifying the influence of OM on microorganism mobility in porous media such as filter beds, which may be used for either drinking water treatment or waste water treatment. In the wider environment study findings have potential to allow more confident predictions of the mobility of sewage derived pathogens discharging to groundwater.

Developing an integrated hydrograph separation and lumped modelling approach to quantifying hydrological pathways in Irish river catchments

An appreciation of the quantity of streamflow derived from the main hydrological pathways involved in transporting diffuse contaminants is critical when addressing a wide range of water resource management issues. In order to assess hydrological pathway contributions to streams, it is necessary to provide feasible upper and lower bounds for flows in each pathway. An important first step in this process is to provide reliable estimates of the slower responding groundwater pathways and subsequently the quicker overland and interflow pathways. This paper investigates the effectiveness of a multi-faceted approach applying different hydrograph separation techniques, supplemented by lumped hydrological modelling, for calculating the Baseflow Index (BFI), for the development of an integrated approach to hydrograph separation. A semi-distributed, lumped and deterministic rainfall runoff model known as NAM has been applied to ten catchments (ranging from 5 to 699 km2). While this modelling approach is useful as a validation method, NAM itself is also an important tool for investigation. These separation techniques provide a large variation in BFI, a difference of 0.741 predicted for BFI in a catchment with the less reliable fixed and sliding interval methods and local minima turning point methods included. This variation is reduced to 0.167 with these methods omitted. The Boughton and Eckhardt algorithms, while quite subjective in their use, provide quick and easily implemented approaches for obtaining physically realistic hydrograph separations. It is observed that while the different separation techniques give varying BFI values for each of the catchments, a recharge coefficient approach developed in Ireland, when applied in conjunction with the Master recession Curve Tabulation method, predict estimates in agreement with those obtained using the NAM model, and these estimates are also consistent with the study catchments’ geology. These two separation methods, in conjunction with the NAM model, were selected to form an integrated approach to assessing BFI in catchments.

An Integrated Approach to Quantifying Groundwater and Surface Water Contributions of Stream Flow

The management of water resources in Ireland prior to the Water Framework Directive (WFD) has focussed on surface water and groundwater as separate entities. A critical element to the successful implementation of the
WFD is to improve our understanding of the interaction between the two and flow mechanisms by which groundwaters discharge to surface waters. An improved understanding of the contribution of groundwater to surface water is required for the classification of groundwater body status and the determination of groundwater quality thresholds. The results of the study will also have a wider application to many areas of the WFD.
A subcommittee of the WFD Groundwater Working Group (GWWG) has been formed to develop a methodology to estimate the groundwater contribution to Irish Rivers. The group has selected a number of analytical techniques to quantify components of stream flow in an Irish context (Master Recession Curve, Unit Hydrograph, Flood Studies Report methodologies and
hydrogeological analytical modelling). The components of stream flow that can be identified include deep groundwater, intermediate and overland. These analyses have been tested on seven pilot catchments that have a variety of hydrogeological settings and have been used to inform and constrain a mathematical model. The mathematical model used was the NAM (NedbØr-AfstrØmnings-Model) rainfall-runoff model which is a module of DHIs MIKE 11 modelling suite. The results from these pilot catchments have been used to develop a decision model based on catchment descriptors from GIS datasets for the selection of NAM parameters. The datasets used include the mapping of aquifers, vulnerability and subsoils, soils, the Digital Terrain Model, CORINE and lakes. The national coverage of the GIS datasets has allowed the extrapolation of the mathematical model to regional catchments across Ireland.

A simple inhibition coefficient for quantifying potency of biocontrol agents against plant-pathogenic fungi

Microbial interactions depend on a range of biotic and environmental variables, and are both dynamic and unpredictable. For some purposes, and under defined conditions, it is nevertheless imperative to evaluate the inhibitory efficacy of microbes, such as those with potential as biocontrol agents. We selected six, phylogenetically diverse microbes to determine their ability to inhibit the ascomycete Fusarium
coeruleum, a soil-dwelling pathogen of potato tubers that causes the storage disease dry rot. Interaction assays, where colony development was quantified (for both fungal pathogen and potential control agents), were therefore carried out on solid media. The key parameters that contributed to, and were indicative of, inhibitory efficacy were identified as: fungal growth-rates (i) prior to contact with the biocontrol
agent and (ii) if/once contact with the biocontrol agent was established (i.e. in the zone of mixed
culture), and (iii) the ultimate distance traveled by the fungal mycelium. It was clear that there was no correlation between zones of fungal inhibition and the overall reduction in the extent of fungal colony development. An inhibition coefficient was devised which incorporated the potential contributions of distal inhibition of fungal growth-rate; prevention of mycelium development in the vicinity of the biocontrol
agent; and ability to inhibit plant-pathogen growth-rate in the zone of mixed culture (in a ratio of 2:2:1). The values derived were 84.2 for Bacillus subtilis (QST 713), 74.0 for Bacillus sp. (JC12GB42), 30.7 for Pichia anomala (J121), 19.3 for Pantoea agglomerans (JC12GB34), 13.9 for Pantoea sp. (S09:T:12), and
21.9 (indicating a promotion of fungal growth) for bacterial strain (JC12GB54). This inhibition coefficient, with a theoretical maximum of 100, was consistent with the extent of F. coeruleum-colony development (i.e. area, in cm2) and assays of these biocontrol agents carried out previously against Fusarium
spp., and other fungi. These findings are discussed in relation to the dynamics and inherent complexity of natural ecosystems, and the need to adapt models for use under specific sets of conditions.

Magnetic mirror cavities as terahertz radiation sources and a means of quantifying radiation friction

We propose a radiation source based on a magnetic mirror cavity. Relativistic electrons are simulated entering the cavity and their trajectories and resulting emission spectra are calculated. The uniformity of the particle orbits is found to result in a frequency comb in terahertz range, the precise energies of which are tunable by varying the electron's gamma-factor. For very high energy particles, radiation friction causes the spectral harmonics to broaden and we suggest this as a possible way to verify competing classical equations of motion.

Quantifying heritable variation in fitness-related traits of wild, farmed and hybrid Atlantic salmon families in a wild river environment

Farmed fish are typically genetically different from wild conspecifics. Escapees from fish farms may contribute one-way gene flow from farm to wild gene pools, which can depress population productivity, dilute local adaptations and disrupt coadapted gene complexes. Here, we reanalyse data from two experiments (McGinnity et al., 1997, 2003) where performance of Atlantic salmon (Salmo salar) progeny originating from experimental crosses between farm and wild parents (in three different cohorts) were measured in a natural stream under common garden conditions. Previous published analyses focussed on group-level differences but did not account for pedigree structure, as we do here using modern mixed-effect models. Offspring with one or two farm parents exhibited poorer survival in their first and second year of life compared with those with two wild parents and these group-level inferences were robust to excluding outlier families. Variation in performance among farm, hybrid and wild families was generally similar in magnitude. Farm offspring were generally larger at all life stages examined than wild offspring, but the differences were moderate (5–20%) and similar in magnitude in the wild versus hatchery environments. Quantitative genetic analyses conducted using a Bayesian framework revealed moderate heritability in juvenile fork length and mass and positive genetic correlations (>0.85) between these morphological traits. Our study confirms (using more rigorous statistical techniques) previous studies showing that offspring of wild fish invariably have higher fitness and contributes fresh insights into family-level variation in performance of farm, wild and hybrid Atlantic salmon families in the wild. It also adds to a small, but growing, number of studies that estimate key evolutionary parameters in wild salmonid populations. Such information is vital in modelling the impacts of introgression by escaped farm salmon.

A novel method of quantifying root exudation in the presence of soil microflora

A microcosm is described in which root exudation may be estimated in the presence of microorganisms. Ryegrass seedlings are grown in microcosms in which roots were spatially separated from a microbial inoculant by a Millipore membrane. Seedlings grown in the microcosms were labelled with [¹⁴C]-CO₂, and the fate of the label within the plant and rhizosphere was determined. Inoculation of the microcosms with Cladosporium resinae increased net fixation of the [¹⁴C] label compared to plants grown under sterile conditions. Inoculation also increased root exudation. The use of the microcosm was illustrated and its applications discussed. © 1991 Kluwer Academic Publishers.

Quantifying consumer portion control practices. A cross-sectional study

The use of portion control practices has rarely been quantified. The present study aimed to: (1) explore which portion control practices are actually used by the general population and their association with cognitive restraint, demographic background and general health interest (GHI), and (2) examine how the usage of portion control practices predicts the estimated consumption of an energy dense food (i.e. pizza). Twenty-two portion control practices were rated in terms of their frequency of use from 'never' to 'very often' by a representative sample of 1012 consumers from the island of Ireland. Three factors were extracted and named: measurement-strategy scale, eating-strategy scale, and purchasing-strategy scale. The eating-strategy scale score was the highest, while the measurement-strategy scale carried the lowest frequency score. For each strategy scale score, the strongest predictor was GHI, followed by gender. Having higher GHI and being female were independently associated with more frequent portion control. Both the eating-strategy scale score and the purchasing-strategy scale score were negatively associated with pizza portion size consumption estimates. In conclusion, while this study demonstrates that the reported use of portion control practices is low, the findings provide preliminary evidence for their validity. Further studies are needed to explore how portion control practices are used in different kinds of portion size decisions and what their contribution is to the intake of food over an extended period of time.