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.

Structural and functional basis for ADP-ribose and poly(ADP-ribose) binding by viral macro domains.

Macro domains constitute a protein module family found associated with specific histones and proteins involved in chromatin metabolism. In addition, a small number of animal RNA viruses, such as corona- and toroviruses, alphaviruses, and hepatitis E virus, encode macro domains for which, however, structural and functional information is extremely limited. Here, we characterized the macro domains from hepatitis E virus, Semliki Forest virus, and severe acute respiratory syndrome coronavirus (SARS-CoV). The crystal structure of the SARS-CoV macro domain was determined at 1.8-Å resolution in complex with ADP-ribose. Information derived from structural, mutational, and sequence analyses suggests a close phylogenetic and, most probably, functional relationship between viral and cellular macro domain homologs. The data revealed that viral macro domains have relatively poor ADP-ribose 1"-phosphohydrolase activities (which were previously proposed to be their biologically relevant function) but bind efficiently free and poly(ADP-ribose) polymerase 1-bound poly(ADP-ribose) in vitro. Collectively, these results suggest to further evaluate the role of viral macro domains in host response to viral infection.

Application of a Generic Curriculum Change Management Process to Motivate and Excite Students

The School of Mechanical and Aerospace Engineering at Queen’s University Belfast is committed to enhancing the quality of student learning. A plan to implement curriculum change around this goal has been formulated and is already several years underway. A specific part of the plan involved instigating a first year introductory module to engage the students in the practice of their engineering discipline. The complicated nature of devising this type of module with regard to objectives, resources, timeframe and the number of students involved meant that a very systematic approach had to be adopted. This paper presents the simple but definitive change management process that facilitated in the creation of a first year Introduction to Engineering module. The generic nature of this process is described and its application to other facets of curriculum change is discussed. Within this process the importance of collaboration to establish a forward momentum is emphasised. This enables academic staff to progress as a group and build curriculum development based on their own experiences, expertise and established practice

Genetic association analyses of non-synonymous single nucleotide polymorphisms in diabetic nephropathy

Aims/hypothesis: Diabetic nephropathy, characterised by persistent proteinuria, hypertension and progressive kidney failure, affects a subset of susceptible individuals with diabetes. It is also a leading cause of end-stage renal disease (ESRD). Non-synonymous (ns) single nucleotide polymorphisms (SNPs) have been reported to contribute to genetic susceptibility in both monogenic disorders and common complex diseases. The objective of this study was to investigate whether nsSNPs are involved in susceptibility to diabetic nephropathy using a case-control design.

Methods: White type 1 diabetic patients with (cases) and without (controls) nephropathy from eight centres in the UK and Ireland were genotyped for a selected subset of nsSNPs using Illumina's GoldenGate BeadArray assay. A ? 2 test for trend, stratified by centre, was used to assess differences in genotype distribution between cases and controls. Genomic control was used to adjust for possible inflation of test statistics, and the False Discovery Rate method was used to account for multiple testing.

Results: We assessed 1,111 nsSNPs for association with diabetic nephropathy in 1,711 individuals with type 1 diabetes (894 cases, 817 controls). A number of SNPs demonstrated a significant difference in genotype distribution between groups before but not after correction for multiple testing. Furthermore, neither subgroup analysis (diabetic nephropathy with ESRD or diabetic nephropathy without ESRD) nor stratification by duration of diabetes revealed any significant differences between groups.

Conclusions/interpretation: The nsSNPs investigated in this study do not appear to contribute significantly to the development of diabetic nephropathy in patients with type 1 diabetes.

The cost of water from an autonomous wave-powered desalination plant

A techno-economic model of an autonomous wave-powered desalination plant is developed and indicates that fresh water can be produced for as little as £0.45/m3. The advantages of an autonomous wave-powered desalination plant are also discussed indicating that the real value of the system is enhanced due to its flexibility for deployment and reduced environmental impact. The modelled plant consists of the Oyster wave energy converter, conventional reverse osmosis membranes and a pressure exchanger–intensifier for energy recovery. A time-domain model of the plant is produced using wave-tank experimentation to calibrate the model of Oyster, manufacturer's data for the model of the reverse osmosis membranes and a hydraulic model of the pressure exchanger–intensifier. The economic model of the plant uses best-estimate cost data which are reduced to annualised costs to facilitate the calculation of the cost of water. Finally, the barriers to the deployment of this technology are discussed, but they are not considered insurmountable.

An autonomous wave-powered desalination system

The potential for an autonomous wave-powered desalination system is considered and it is identified that the most promising configuration is a reverse osmosis (RO) plant utilising a pressure exchanger-intensifier for energy recovery. A numerical model of the RO plant with a pressure exchanger-intensifier is developed that shows that a specific energy consumption of less than 2.0 kW h/m3 over a wide range of sea-water feed conditions, making it particularly suitable for use with a variable power source such as wave energy. A numerical model of the combined wave-power and desalination plant is also developed that shows that it is possible to supply the desalination plant with sea-water directly pressurised by the wave energy converter, eliminating the cost and energy losses associated with converting the energy into electricity and back to pressurised water. For a typical sea-state the specific hydraulic energy consumption of the desalination plant is estimated to be 1.85 kW h/m3 whilst maintaining a recovery-ratio of less than 25 to 35% to avoid the need for chemical pre-treatment to eliminate scaling problems. It is suggested that the economic potential for wave-powered desalination depends on these energy and cost savings more than compensating for the reduction in membrane life that occurs with variable feed conditions.

Analysis of the nearshore wave energy resource

Earlier studies have indicated that the gross nearshore wave energy resource is significantly smaller than the gross offshore wave energy resource implying that the deployment of wave energy converters in the nearshore is unlikely to be economic. However, it is argued that the gross wave energy resource is not an appropriate measure for determining the productivity of a wave farm and an alternative measure, the exploitable wave energy resource, is proposed. Calculation of a site's potential using the exploitable wave energy resource is considered superior because it accounts for the directional distribution of the incident waves and the wave energy plant rating that limits the power capture in highly energetic sea-states. A third-generation spectral wave model is used to model the wave transformation from deep water to a nearshore site in a water depth of 10 m. It is shown that energy losses result in a reduction of less than 10% of the net incident wave power. Annual wave data for the North Atlantic coast of Scotland is analysed and indicates that whilst the gross wave energy resource has reduced significantly by the 10 m depth contour, the exploitable wave energy resource is reduced by 7 and 22% for the two sites analysed. This limited reduction in exploitable wave energy resource means that for many exposed coasts, nearshore sites offer similar potential for exploitation of the wave energy resource as offshore sites.