A comprehensive investigation of the synthesis of prebiotic galactooligosaccharides by whole cells of Bifidobacterium bifidum NCIMB 41171

The synthesis of galactooligosaccharides (GOS) by whole cells of Bifidobacterium bifidum NCIMB 41171 was investigated by developing a set of mathematical models. These were second order polynomial equations, which described responses related to the production of GOS constituents, the selectivity of lactose conversion into GOS, and the relative composition of the produced GOS mixture, as a function of the amount of biocatalyst, temperature, initial lactose concentration, and time. The synthesis reactions were followed for up to 36 h. Samples were withdrawn every 4 h, tested for β-galactosidase activity, and analysed for their carbohydrate content. GOS synthesis was well explained by the models, which were all significant (P < 0.001). The GOS yield increased as temperature increased from 40 °C to 60 °C, as transgalactosylation became more pronounced compared to hydrolysis. The relative composition of GOS produced changed significantly with the initial lactose concentration (P < 0.001); higher ratios of tri-, tetra-, and penta-galactooligosaccharides to transgalactosylated disaccharides were obtained as lactose concentration increased. Time was a critical factor, as a balanced state between GOS synthesis and hydrolysis was roughly attained in most cases between 12 and 20 h, and was followed by more pronounced GOS hydrolysis than synthesis.

An integrated dynamic whole life costing analysis for air distribution systems

Air distribution systems are one of the major electrical energy consumers in air-conditioned commercial buildings which maintain comfortable indoor thermal environment and air quality by supplying specified amounts of treated air into different zones. The sizes of air distribution lines affect energy efficiency of the distribution systems. Equal friction and static regain are two well-known approaches for sizing the air distribution lines. Concerns to life cycle cost of the air distribution systems, T and IPS methods have been developed. Hitherto, all these methods are based on static design conditions. Therefore, dynamic performance of the system has not been yet addressed; whereas, the air distribution systems are mostly performed in dynamic rather than static conditions. Besides, none of the existing methods consider any aspects of thermal comfort and environmental impacts. This study attempts to investigate the existing methods for sizing of the air distribution systems and proposes a dynamic approach for size optimisation of the air distribution lines by taking into account optimisation criteria such as economic aspects, environmental impacts and technical performance. These criteria have been respectively addressed through whole life costing analysis, life cycle assessment and deviation from set-point temperature of different zones. Integration of these criteria into the TRNSYS software produces a novel dynamic optimisation approach for duct sizing. Due to the integration of different criteria into a well- known performance evaluation software, this approach could be easily adopted by designers in busy nature of design. Comparison of this integrated approach with the existing methods reveals that under the defined criteria, system performance is improved up to 15% compared to the existing methods. This approach is interpreted as a significant step forward reaching to the net zero emission building in future.

A wide-angle X-ray study of the development of molecular orientation in crosslinked natural rubber

Molecular orientation parameters have been measured for the non-crystalline component of crosslinked natural rubber samples deformed in uniaxial tension as a function of the extension ratio and of temperature. The orientation parapeters 〈P2(cosα)〉 and 〈P4(cosα)〉 were obtained by an analysis of the anisotropy of the wide-angle X-ray scattering functions. For the measurements made at high temperatures the level of crystallinity detected was negligible and the orientation-strain behaviour could be compared directly with the predictions of molecular models of rubber elasticity. The molecular orientation behaviour with strain was found to be at variance with the estimates of the affine model particularly at low and moderate strains. Extension of the crosslinked rubber at room temperature led to strain-crystallization and measurements of both the molecular orientation of the non-crystalline chains and the degree of crystallinity during extension and relaxation enabled the role of the crystallites in the deformation process to be considered in detail. The intrinsic birefringence of the non-crystalline component was estimated, through the use of the 〈P2(cosα)〉 values obtained from X-ray scattering measurements, to be 0.20±0.02.

Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array

Background A whole-genome genotyping array has previously been developed for Malus using SNP data from 28 Malus genotypes. This array offers the prospect of high throughput genotyping and linkage map development for any given Malus progeny. To test the applicability of the array for mapping in diverse Malus genotypes, we applied the array to the construction of a SNPbased linkage map of an apple rootstock progeny. Results Of the 7,867 Malus SNP markers on the array, 1,823 (23.2 %) were heterozygous in one of the two parents of the progeny, 1,007 (12.8 %) were heterozygous in both parental genotypes, whilst just 2.8 % of the 921 Pyrus SNPs were heterozygous. A linkage map spanning 1,282.2 cM was produced comprising 2,272 SNP markers, 306 SSR markers and the S-locus. The length of the M432 linkage map was increased by 52.7 cM with the addition of the SNP markers, whilst marker density increased from 3.8 cM/marker to 0.5 cM/marker. Just three regions in excess of 10 cM remain where no markers were mapped. We compared the positions of the mapped SNP markers on the M432 map with their predicted positions on the ‘Golden Delicious’ genome sequence. A total of 311 markers (13.7 % of all mapped markers) mapped to positions that conflicted with their predicted positions on the ‘Golden Delicious’ pseudo-chromosomes, indicating the presence of paralogous genomic regions or misassignments of genome sequence contigs during the assembly and anchoring of the genome sequence. Conclusions We incorporated data for the 2,272 SNP markers onto the map of the M432 progeny and have presented the most complete and saturated map of the full 17 linkage groups of M. pumila to date. The data were generated rapidly in a high-throughput semi-automated pipeline, permitting significant savings in time and cost over linkage map construction using microsatellites. The application of the array will permit linkage maps to be developed for QTL analyses in a cost-effective manner, and the identification of SNPs that have been assigned erroneous positions on the ‘Golden Delicious’ reference sequence will assist in the continued improvement of the genome sequence assembly for that variety.

Towards effective water reuse: drivers, challenges and strategies shaping the organisational management of reclaimed water in Jordan

Treated wastewater or reclaimed water is gaining recognition as a valuable water resource around the world. To assess why, where and how water reuse takes place in Jordan, semi-structured interviews were conducted with representatives of 29 key organisations in 2008. The analysis reveals that water scarcity is a key driver for water reuse. However, despite such recognition, reuse was described positively by only a small proportion of the interviewees (n = 6). Negative and neutral perceptions regarding reuse dominated and the research found that this was related to two underlying challenges: (i) the requirement for more intensive management when using reclaimed water compared with freshwater and (ii) concern over societal acceptance of water reuse. These factors were found to be associated with the risks posed to humans and their environments, combined with negative emotional and cultural responses to human waste and its applications. Numerous strategies are identified that are employed by organisations to overcome these challenges. Wastewater treatment, regulation, monitoring, the mixing of treated effluent with freshwater and limited public discussion of water reuse are all employed to achieve maximum use of reclaimed water. Each strategy presents benefits of sort, but some may paradoxically also inhibit optimal use of reclaimed water. Careful modifications to the existing strategies of Jordanian agencies, such as more open discussion of reuse, could lead to greater social, economic and environmental gains.

Whole life carbon – a building case study

There is potential to reduce both operational and embodied greenhouse gas emission from buildings. To date the focus has been on reducing the operational element, although given the urgency of carbon reductions, it may be more beneficial to consider upfront embodied carbon reductions. This paper describes a case study on the whole life carbon cycle of a warehouse building in Swindon, UK. It examines the relationship between embodied carbon (Ec) and operational carbon (Oc), the proportions of Ec from the structural and non-structural elements, carbon benchmarking of the structure, the value of ‘cradle to site’ or ‘cradle to grave’ assessments and the significance of the timing of emissions during the life of the building. The case study indicates that Ec was dominant for the building and that the structure was responsible for more than half of the Ec. Weighting of future emissions appears to be an important factor to consider. The PAS 2050 reduction factors had only a modest effect but weighting to allow for future decarbonisation of the national grid energy supply had a large effect. This suggests that future operational carbon emissions are being overestimated compared to embodied.

Whole-brain functional connectivity during emotional word classification in medication-free Major Depressive Disorder: abnormal salience circuitry and relations to positive emotionality

Major Depressive Disorder (MDD) has been associated with biased processing and abnormal regulation of negative and positive information, which may result from compromised coordinated activity of prefrontal and subcortical brain regions involved in evaluating emotional information. We tested whether patients with MDD show distributed changes in functional connectivity with a set of independently derived brain networks that have shown high correspondence with different task demands, including stimulus salience and emotional processing. We further explored if connectivity during emotional word processing related to the tendency to engage in positive or negative emotional states. In this study, 25 medication-free MDD patients without current or past comorbidity and matched controls (n=25) performed an emotional word-evaluation task during functional MRI. Using a dual regression approach, individual spatial connectivity maps representing each subject’s connectivity with each standard network were used to evaluate between-group differences and effects of positive and negative emotionality (extraversion and neuroticism, respectively, as measured with the NEO-FFI). Results showed decreased functional connectivity of the medial prefrontal cortex, ventrolateral prefrontal cortex, and ventral striatum with the fronto-opercular salience network in MDD patients compared to controls. In patients, abnormal connectivity was related to extraversion, but not neuroticism. These results confirm the hypothesis of a relative (para)limbic-cortical decoupling that may explain dysregulated affect in MDD. As connectivity of these regions with the salience network was related to extraversion, but not to general depression severity or negative emotionality, dysfunction of this network may be responsible for the failure to sustain engagement in rewarding behavior.

Modelling the economics of farm-based anaerobic digestion in a UK whole-farm context

Anaerobic digestion (AD) technologies convert organic wastes and crops into methane-rich biogas for heating, electricity generation and vehicle fuel. Farm-based AD has proliferated in some EU countries, driven by favourable policies promoting sustainable energy generation and GHG mitigation. Despite increased state support there are still few AD plants on UK farms leading to a lack of normative data on viability of AD in the whole-farm context. Farmers and lenders are therefore reluctant to fund AD projects and policy makers are hampered in their attempts to design policies that adequately support the industry. Existing AD studies and modelling tools do not adequately capture the farm context within which AD interacts. This paper demonstrates a whole-farm, optimisation modelling approach to assess the viability of AD in a more holistic way, accounting for such issues as: AD scale, synergies and conflicts with other farm enterprises, choice of feedstocks, digestate use and impact on farm Net Margin. This modelling approach demonstrates, for example, that: AD is complementary to dairy enterprises, but competes with arable enterprises for farm resources. Reduced nutrient purchases significantly improve Net Margin on arable farms, but AD scale is constrained by the capacity of farmland to absorb nutrients in AD digestate.

A Brassica exon array for whole-transcript gene expression profiling

Affymetrix GeneChip (R) arrays are used widely to study transcriptional changes in response to developmental and environmental stimuli. GeneChip (R) arrays comprise multiple 25-mer oligonucleotide probes per gene and retain certain advantages over direct sequencing. For plants, there are several public GeneChip (R) arrays whose probes are localised primarily in 39 exons. Plant whole-transcript (WT) GeneChip (R) arrays are not yet publicly available, although WT resolution is needed to study complex crop genomes such as Brassica, which are typified by segmental duplications containing paralogous genes and/or allopolyploidy. Available sequence data were sampled from the Brassica A and C genomes, and 142,997 gene models identified. The assembled gene models were then used to establish a comprehensive public WT exon array for transcriptomics studies. The Affymetrix GeneChip (R) Brassica Exon 1.0 ST Array is a 5 mu M feature size array, containing 2.4 million 25-base oligonucleotide probes representing 135,201 gene models, with 15 probes per gene distributed among exons. Discrimination of the gene models was based on an E-value cut-off of 1E(-5), with <= 98 sequence identity. The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference Brassica rapa line (R-o-18), and categorisation by Gene Ontologies (GO) based on gene orthology with Arabidopsis thaliana. Technical validation involved comparison of the exon array with a 60-mer array platform using the same starting RNA samples. The 135 k Brassica Exon Array is a robust platform. All data relating to the array design and probe identities are available in the public domain and are curated within the BrassEnsembl genome viewer at http://www.brassica.info/BrassEnsembl/index.html.

Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing

Whole-genome sequencing (WGS) could potentially provide a single platform for extracting all the information required to predict an organism’s phenotype. However, its ability to provide accurate predictions has not yet been demonstrated in large independent studies of specific organisms. In this study, we aimed to develop a genotypic prediction method for antimicrobial susceptibilities. The whole genomes of 501 unrelated Staphylococcus aureus isolates were sequenced, and the assembled genomes were interrogated using BLASTn for a panel of known resistance determinants (chromosomal mutations and genes carried on plasmids). Results were compared with phenotypic susceptibility testing for 12 commonly used antimicrobial agents (penicillin, methicillin, erythromycin, clindamycin, tetracycline, ciprofloxacin, vancomycin, trimethoprim, gentamicin, fusidic acid, rifampin, and mupirocin) performed by the routine clinical laboratory. We investigated discrepancies by repeat susceptibility testing and manual inspection of the sequences and used this information to optimize the resistance determinant panel and BLASTn algorithm. We then tested performance of the optimized tool in an independent validation set of 491 unrelated isolates, with phenotypic results obtained in duplicate by automated broth dilution (BD Phoenix) and disc diffusion. In the validation set, the overall sensitivity and specificity of the genomic prediction method were 0.97 (95% confidence interval [95% CI], 0.95 to 0.98) and 0.99 (95% CI, 0.99 to 1), respectively, compared to standard susceptibility testing methods. The very major error rate was 0.5%, and the major error rate was 0.7%. WGS was as sensitive and specific as routine antimicrobial susceptibility testing methods. WGS is a promising alternative to culture methods for resistance prediction in S. aureus and ultimately other major bacterial pathogens.

Fold-change detection in a whole-pathway model of Escherichia coli chemotaxis

There has been recent interest in sensory systems that are able to display a response which is proportional to a fold change in stimulus concentration, a feature referred to as fold-change detection (FCD). Here, we demonstrate FCD in a recent whole-pathway mathematical model of Escherichia coli chemotaxis. FCD is shown to hold for each protein in the signalling cascade and to be robust to kinetic rate and protein concentration variation. Using a sensitivity analysis, we find that only variations in the number of receptors within a signalling team lead to the model not exhibiting FCD. We also discuss the ability of a cell with multiple receptor types to display FCD and explain how a particular receptor configuration may be used to elucidate the two experimentally determined regimes of FCD behaviour. All findings are discussed in respect of the experimental literature.

A Lab-in-a-briefcase for rapid prostate specific antigen (PSA) screening from whole blood

We present a new concept for rapid and fully portable Prostate Specific Antigen (PSA) measurement, termed “Lab-in-a-Briefcase”, which integrates an affordable microfluidic ELISA platform utilising a melt-extruded fluoropolymer Micro Capillary Film (MCF) containing 10 bore, 200 μm internal diameter capillaries, a disposable multi-syringe aspirator (MSA) plus a sample tray pre-loaded with all required immunoassay reagents, and a portable film scanner for colorimetric signal digital quantitation. Each MSA can perform 10 replicate microfluidic immunoassays on 8 samples, allowing 80measurements to be made in less than 15 minutes based on semi-automated operation and norequirement of additional fluid handling equipment. An assay was optimised for measurement of a clinically relevant range of PSA from 0.9 to 60.0 ng/ml in 15 minutes with CVs in the order of 5% based on intra-assay variability when read using a consumer flatbed film scanner. The PSA assay performance in the MSA remained robust in the presence of undiluted or 1:2 diluted human serum or whole blood, and the matrix effect could simply be overcome by extending sample incubation times. The PSA "Lab-in-a-briefcase" is particularly suited to a low-resource health setting where diagnostic labs and automated immunoassay systems are not accessible, by allowing PSA measurement outside the laboratory using affordable equipment.

The greater whole: towards a synthesis of system dynamics and soft systems methodology

This paper makes a theoretical case for using these two systems approaches together. The theoretical and methodological assumptions of system dynamics (SD) and soft system methodology (SSM) are briefly described and a partial critique is presented. SSM generates and represents diverse perspectives on a problem situation and addresses the socio-political elements of an intervention. However, it is weak in ensuring `dynamic coherence'. consistency between the intuitive behaviour resulting from proposed changes and behaviour deduced from ideas on causal structure. Conversely, SD examines causal structures and dynamic behaviours. However, whilst emphasising the need for a clear issue focus, it has little theory for generating and representing diverse issues. Also, there is no theory for facilitating sensitivity to socio-political elements. A synthesis of the two called ‘Holon Dynamics' is proposed. After an SSM intervention, a second stage continues the socio-political analysis and also operates within a new perspective which values dynamic coherence of the mental construct - the holon - which is capable of expressing the proposed changes. A model of this holon is constructed using SD and the changes are thus rendered `systemically desirable' in the additional sense that dynamic consistency has been confirmed. The paper closes with reflections on the proposal and the need for theoretical consistency when mixing tools is emphasised.