Evaluation of predicted network modules in yeast metabolism using NMR-based metabolite profiling

Genome-scale metabolic models promise important insights into cell function. However, the definition of pathways and functional network modules within these models, and in the biochemical literature in general, is often based on intuitive reasoning. Although mathematical methods have been proposed to identify modules, which are defined as groups of reactions with correlated fluxes, there is a need for experimental verification. We show here that multivariate statistical analysis of the NMR-derived intra- and extracellular metabolite profiles of single-gene deletion mutants in specific metabolic pathways in the yeast Saccharomyces cerevisiae identified outliers whose profiles were markedly different from those of the other mutants in their respective pathways. Application of flux coupling analysis to a metabolic model of this yeast showed that the deleted gene in an outlying mutant encoded an enzyme that was not part of the same functional network module as the other enzymes in the pathway. We suggest that metabolomic methods such as this, which do not require any knowledge of how a gene deletion might perturb the metabolic network, provide an empirical method for validating and ultimately refining the predicted network structure.

Anti-sized reed bed system for animal wastewater treatment: a comparative study

This paper presents a comparative study on the treatment of high-strength animal wastewater in two parallel lab-scale constructed reed bed systems, progressively-sized system and anti-sized system, which have same configuration but different arrangement of bed media. The reed bed systems were operated in a tidal flow pattern to treat diluted pig slurry. Detailed analyses were carried out for the removal of some key pollutants including COD, BOD5, NH4-N, P and suspended solids. The results showed that both systems have considerable capacity for the removal of solids, organic matter and inorganic nutrients. The formation of biofilms on the surfaces of gravel media in both reed bed systems was monitored by scanning selected gravel samples using scanning electron microscopy. In general, no significant difference was detected with regard to the percentage pollutant removal in the systems. However, the anti-sized system demonstrated a clear advantage in its ability to slow down the clogging of bed media and avoid the impairment of long-term functioning and sustainability of the beds. A conceptual model was developed to predict the occurrence of the clogging. The validity of the model was tested using data from this study and from the literatures.

Purification capacity of a highly loaded laboratory scale tidal flow reed bed system with effluent recirculation

The purification capacity of a laboratory scale tidal flow reed bed system with final effluent recirculation at a ratio of 1:1 was investigated in this study. In particular, this four-stage reed bed system was highly loaded with strong agricultural wastewater. Under the hydraulic and organic loading rates as high as 0.43 m3/m2d and 1055 gCOD/m2d, respectively, the average removal efficiencies of COD, BOD5, SS, NH4-N and P were 77%, 78%, 66%, 62% and 38%. Even with the high loading rates, approximately 30% of NH4-N was converted into NO2-N and NO3-N from the mid-stage of the system where nitrification took place. The results suggest that the multi-stage reed bed system could be employed to treat strong wastewater under high loading, especially for the substantive mass removal of solids, organic matter and ammoniacal-nitrogen. Tidal flow combined with effluent recirculation is a favourable operation strategy to achieve this objective.

Influence of prolonged hospitalization on overall bed occupancy: a five-year single-centre study

Background: Effective bed use is crucial to an efficient NHS. Current targets suggest a decrease in mean occupancy as the most appropriate method of improving overall efficiency. The elderly and those suffering from complex medical problems are thought to account for a high proportion of overall bed occupancy.

Aim: To assess the effect of prolonged hospital stay (>100 days) on overall bed occupancy in a modern teaching hospital.

Design: Retrospective analysis.

Methods: Analysis of all admission episodes (n = 117 178) over a five-year period in a large teaching hospital in a single UK region, serving a population of approximately 200 000. A logistic regression multi-factorial model was used to assess the effect of demographic and diagnostic variables on duration of stay.

Results: A prolonged stay (>100 days) was seen in 648 admission episodes (0.6%). These accounted for 11% of the overall bed occupancy over the 5-year period. Excluding all prolonged admission episodes from our analysis made no difference to the overall median length of stay.

Discussion: Prolonged hospitalizations have a significant impact on bed occupancy. Targeting these very long (>100 days) hospital stays may better improve overall efficiency, compared to targeting mean or median length of stay.

Use of the multispecies freshwater biomonitor to assess behavioral changes of Corophium volutator (Pallas, 1766) (Crustacea, Amphipoda) in response to toxicant exposure in sediment

Automated sediment toxicity testing and biomonitoring has grown rapidly. This study tested the suitability of the marine amphipod Corophium volutator (Pallas, 1766) for sediment biomonitoring using the Multispecies Freshwater Biomonitor (MFB). Two experiments were undertaken to (1) characterize individual behaviors of C. volutator using the MFB and (2) examine behavioral changes in response to sediment spiked with the pesticide Bioban. Four behaviors were visually identified (walking, swimming, grooming and falling) and characterized in the MFB as different patterns of locomotor activity (0-2 Hz range). Ventilation was not visually observed but was detected by the MFB (2-8 Hz). No clear diel activity patterns were detected. The MFB detected an overall increase in C. volutator locomotor activity after Bioban addition to the sediments (56, 100, 121 mg kg(-1)). C. volutator was more active (both locomotion and ventilation) in the water column than the spiked sediment. C. volutator appears a sensitive and appropriate species for behavioral sediment toxicity assessment and biomonitoring. (c) 2005 Elsevier Inc. All rights reserved.

Inhibitor profiling of the Pseudomonas aeruginosa virulence factor LasB using N-alpha mercaptoamide template-based inhibitors

We report on the synthesis and biological evaluation of a focussed library of N-alpha mercaptoamide containing dipeptides as inhibitors of the zinc metallopeptidase Pseudomonas aeruginosa elastase (LasB, EC 3.4.24.26). The aim of the study was to derive an inhibitor profile for LasB with regard to mapping the S´1 binding site of the enzyme. Consequently, a focussed library of 160 members has been synthesised, using standard Fmoc-solid phase methods (on a Rink-amide resin), in which a subset of amino acids including examples of those with basic (Lys, Arg), aromatic (Phe, Trp), large aliphatic (Val, Leu) and acidic (Asp, Glu) side-chains populated the P´2 position of the inhibitor sequence and all 20 natural amino acids were incorporated, in turn, at the P´1 position. The study has revealed a preference for aromatic and/or large aliphatic amino acids at P´1 and a distinct bias against acidic residues at P´2. Ten inhibitor sequences were discovered that exhibited sub to low micromolar Ki values.

Under-water scene investigation using ground penetrating radar (GPR) in the search for a sunken jet ski, Northern Ireland

A search for a submerged jet ski and the lost limb of its driver involved in a collision with a speedboat was made in a shallow lake in Northern Ireland. The location of both was crucial to establishing events at the time of the accident. Local intelligence suggested both objects were likely to be partially-buried by lacustrine silt. To avoid sediment churning, this required non-invasive, completely non-destructive assessment and mapping of the scene. A MALA RAMAC ground-penetrating radar system (GPR) mounted on floats for surveying from walkways and jetties or placed in a small rubber dinghy for offshore profiling was used. A grid was established and each line surveyed with 100, 200 and 400MHz antennae. In waters over 6m deep GPR data showed the form of the lake floor but excessive ringing occurred in the data. In waters less than 6m deep ringing diminished on both 100 and 200MHz data, the latter displaying the best trade-off between depth penetration and horizontal object resolution. 400MHz data failed to be of use in waters over 2m deep and at these depths showed only limited improvement of image quality compared to 200MHz data. Surface objects such as a wooden walkway caused interference on 200 and 400MHz data when antennae were oriented both normal and parallel to survey direction; this may be a function of the low attenuation of radar waves in freshwater, allowing excellent lateral and vertical radar wave penetration. On 200MHz data the damaged jet-ski was clearly imaged in a location that contradicted the speedboat driver's account of the accident.

Characterisation of fluidised bed granulation processes using in situ Raman spectroscopy

Previous work by the authors Walker et al. [2007b. Fluidised bed characterisation using Raman spectroscopy: applications to pharmaceutical processing. Chemical Engineering Science 62, 3832–3838] illustrated that Raman spectroscopy could be used to provide 3-D maps of the concentration and chemical structure of particles in motion in a fluidised bed, within a relatively short (120 s) time window. Moreover, we reported that the technique, as outlined, has the potential to give detailed in-situ information on how the structure and composition of granules/powders within the fluidised bed (dryer or granulator) vary with the position and evolve with time. In this study we extended the original work by shortening the time window of the Raman spectroscopic analysis to 10 s, which has allowed the in-situ real-time characterisation of a fluidised bed granulation process. Here we show an important new use of the technique which allows in-situ measurement of the composition of the material within the fluidised bed in three spatial dimensions and as a function of time. This is achieved by recording Raman spectra using a probe positioned within the fluidised bed on a long-travel x–y–z stage. In these experiments the absolute Raman intensity is used to provide a direct measure of the amount of any given material in the probed volume, i.e. a particle density. Particle density profiles have been calculated over the granulation time and show how the volume of the fluidised bed decreases with an increase mean granule size. The Raman spectroscopy analysis indicated that nucleation/coalescence in this co-melt fluidised hot melt granulation system occurred over a relatively short time frame (t<30 s). The Raman spectroscopic technique demonstrated accurate correlation with independent granulation experiments which provided particle size distribution analysis. The similarity of the data indicates that the Raman spectra accurately represent solids ratios within the bed, and thus the techniques quantitative capabilities for future use in the pharmaceutical industry.