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.

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.

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.

Twentieth-century global-mean sea-level rise: is the whole greater than the sum of the parts?

Confidence in projections of global-mean sea level rise (GMSLR) depends on an ability to account for GMSLR during the twentieth century. There are contributions from ocean thermal expansion, mass loss from glaciers and ice sheets, groundwater extraction, and reservoir impoundment. Progress has been made toward solving the “enigma” of twentieth-century GMSLR, which is that the observed GMSLR has previously been found to exceed the sum of estimated contributions, especially for the earlier decades. The authors propose the following: thermal expansion simulated by climate models may previously have been underestimated because of their not including volcanic forcing in their control state; the rate of glacier mass loss was larger than previously estimated and was not smaller in the first half than in the second half of the century; the Greenland ice sheet could have made a positive contribution throughout the century; and groundwater depletion and reservoir impoundment, which are of opposite sign, may have been approximately equal in magnitude. It is possible to reconstruct the time series of GMSLR from the quantified contributions, apart from a constant residual term, which is small enough to be explained as a long-term contribution from the Antarctic ice sheet. The reconstructions account for the observation that the rate of GMSLR was not much larger during the last 50 years than during the twentieth century as a whole, despite the increasing anthropogenic forcing. Semiempirical methods for projecting GMSLR depend on the existence of a relationship between global climate change and the rate of GMSLR, but the implication of the authors' closure of the budget is that such a relationship is weak or absent during the twentieth century.