Probabilistic soil moisture projections to assess Great Britain's future clay-related subsidence hazard

Clay-related subsidence is Great Britain’s (GB) most damaging soil-related geohazard, costing the economy up to £500 million per annum. Soil-related geohazard models based on mineralogy and potential soil moisture deficit (PSMD) derived from historic weather data have been used in risk management since the 1990s. United Kingdom Climate Projections (UKCP09) suggest that regions of GB will experience hotter, drier summers and warmer, wetter winters through to 2050. As a result, PSMD fluctuations are expected to increase, exacerbating the shrinkage and swelling of clay soils. A forward-looking approach is now required to mitigate the impacts of future climate on GB’s built environment. We present a framework for incorporating probabilistic projections of PSMD, derived from a version of the UKCP09 stochastic weather generator, into a clay subsidence model. This provides a novel, national-scale thematic model of the likelihood of clay-related subsidence, related to the top 1-1.5m soil layer, for three time periods; baseline (1961-1990), 2030 (2020-2049) and 2050 (2040-2069). Results indicate that much of GB, with the exception of upland areas, will witness significantly higher PSMDs through to the 2050’s. As a result, areas with swelling clay soils will be subject to proportionately increased subsidence hazard. South-east England will likely incur the highest hazard exposure to clay-related subsidence through to 2050. Potential impacts include increased incidence of property foundation subsidence, alongside deterioration and increased failure rates of GB’s infrastructure networks. Future clay-subsidence hazard scenarios provide benefit to many sectors, including: finance, central and local government, residential property markets, utilities and infrastructure operators.EPSR

Soil geohazard mapping for improved asset management of UK local roads

Unclassified roads comprise 60% of the road network in the United Kingdom (UK). The resilience of this locally important network is declining. It is considered by the Institution of Civil Engineers to be “at risk” and is ranked 26th in the world. Many factors contribute to the degradation and ultimate failure of particular road sections. However, several UK local authorities have identified that in drought conditions, road sections founded upon shrink–swell susceptible clay soils undergo significant deterioration compared with sections on non-susceptible soils. This arises from the local road network having little, if any, structural foundations. Consequently, droughts in East Anglia have resulted in millions of pounds of damage, leading authorities to seek emergency governmental funding. This paper assesses the use of soil-related geohazard assessments in providing soil-informed maintenance strategies for the asset management of the locally important road network of the UK. A case study draws upon the UK administrative county of Lincolnshire, where road assessment data have been analysed against mapped clay-subsidence risk. This reveals a statistically significant relationship between road condition and susceptible clay soils. Furthermore, incorporation of UKCP09 future climate projections within the geohazard models has highlighted roads likely to be at future risk of clay-related subsidence

Enhanced visualization of the flat landscape of the Cambridgeshire Fenlands

The Fenlands of East Anglia, England, represent a subtle landscape, where topographic highs rarely exceed 30 m above sea level. However, the fens represent an almost full sequence of Quaternary deposits which, together with islands of Cretaceous and Jurassic outcrops, make the area of geological importance. This feature discusses the advantages of using 3D visualization coupled with high-resolution topographical data, over traditional 2D techniques, when undertaking an analysis of the landscape. Conclusions suggest that the use of 3D visualization will result in a higher level of engagement, particularly when communicating geological information to a wider public

Flexible Nets: a modeling formalism for dynamic systems with uncertain parameters

Funder: FP7 People: Marie-Curie Actions; doi: https://doi.org/10.13039/100011264; Grant(s): 623995Abstract: The modeling of dynamic systems is frequently hampered by a limited knowledge of the system to be modeled and by the difficulty of acquiring accurate data. This often results in a number of uncertain system parameters that are hard to incorporate into a mathematical model. Thus, there is a need for modeling formalisms that can accommodate all available data, even if uncertain, in order to employ them and build useful models. This paper shows how the Flexible Nets (FNs) formalism can be exploited to handle uncertain parameters while offering attractive analysis possibilities. FNs are composed of two nets, an event net and an intensity net, that model the relation between the state and the processes of the system. While the event net captures how the state of the system is updated by the processes in the system, the intensity net models how the speed of such processes is determined by the state of the system. Uncertain parameters are accounted for by sets of inequalities associated with both the event net and the intensity net. FNs are not only demonstrated to be a valuable formalism to cope with system uncertainties, but also to be capable of modeling different system features, such as resource allocation and control actions, in a facile manner

High-energy guanine nucleotides as a signal capable of linking growth to cellular energy status via the control of gene transcription.

This mini-review considers the idea that guanylate nucleotide energy charge acts as an integrative signal for the regulation of gene expression in eukaryotic cells and discusses possible routes for that signal's transduction. Gene expression is intimately linked with cell nutrition and diverse signaling systems serve to coordinate the synthesis of proteins required for growth and proliferation with the prevailing cellular nutritional status. Using short pathways for the inducible and futile consumption of ATP or GTP in engineered cells of Saccharomyces cerevisiae, we have recently shown that GTP levels can also play a role in determining how genes act to respond to changes in cellular energy supply. This review aims to interpret the importance of GTP as an integrative signal in the context of an increasing body of evidence indicating the spatio-temporal complexity of cellular de novo purine nucleotide biosynthesis

Extension of the yeast metabolic model to include iron metabolism and its use to estimate global levels of iron-recruiting enzyme abundance from cofactor requirements.

Metabolic networks adapt to changes in their environment by modulating the activity of their enzymes and transporters; often by changing their abundance. Understanding such quantitative changes can shed light onto how metabolic adaptation works, or how it can fail and lead to a metabolically dysfunctional state. We propose a strategy to quantify metabolic protein requirements for cofactor-utilising enzymes and transporters through constraint-based modelling. The first eukaryotic genome-scale metabolic model to comprehensively represent iron metabolism was constructed, extending the most recent community model of the Saccharomyces cerevisiae metabolic network. Partial functional impairment of the genes involved in the maturation of iron-sulphur (Fe-S) proteins was investigated employing the model and the in silico analysis revealed extensive rewiring of the fluxes in response to this functional impairment, despite its marginal phenotypic effect. The optimal turnover rate of enzymes bearing ion cofactors can be determined via this novel approach; yeast metabolism, at steady state, was determined to employ a constant turnover of its iron-recruiting enzyme at a rate of 3.02 × 10 -11  mmol·(g biomass) -1 ·h  -1 .the Leverhulme Trust (ECF-2016-681 to DD) EC 7th FP (BIOLEDGE Contract no: 289126 to SGO), BBSRC (BRIC2.2 to SGO)

Biomass composition: the "elephant in the room" of metabolic modelling.

Genome-scale stoichiometric models, constrained to optimise biomass production are often used to predict mutant phenotypes. However, for Saccharomyces cerevisiae, the representation of biomass in its metabolic model has hardly changed in over a decade, despite major advances in analytical technologies. Here, we use the stoichiometric model of the yeast metabolic network to show that its ability to predict mutant phenotypes is particularly poor for genes encoding enzymes involved in energy generation. We then identify apparently inefficient energy-generating pathways in the model and demonstrate that the network suffers from the high energy burden associated with the generation of biomass. This is tightly connected to the availability of phosphate since this macronutrient links energy generation and structural biomass components. Variations in yeast's biomass composition, within experimentally-determined bounds, demonstrated that flux distributions are very sensitive to such changes and to the identity of the growth-limiting nutrient. The predictive accuracy of the yeast metabolic model is, therefore, compromised by its failure to represent biomass composition in an accurate and context-dependent manner.The authors gratefully acknowledge the financial support from the Turkish State Planning Organization (DPT09K120520 to BK), TUBITAK (106M444 to BK), BBSRC (BRIC2.2 to SGO), EU 7th Framework Programme (BIOLEDGE Contract No: 289126 to SGO).This is the final version. It was first published by Springer at http://dx.doi.org/10.1007/s11306-015-0819-

Systems biology of energetic and atomic costs in the yeast transcriptome, proteome, and metabolome

Proteins vary in their cost to the cell and natural selection may favour the use of proteins that are cheaper to produce. We develop a novel approach to estimate the amino acid biosynthetic cost based on genome-scale metabolic models, and directly investigate the effects of biosynthetic cost on transcriptomic, proteomic and metabolomic data in _Saccharomyces cerevisiae_. We find that our systems approach to formulating biosynthetic cost produces a novel measure that explains similar levels of variation in gene expression compared with previously reported cost measures. Regardless of the measure used, the cost of amino acid synthesis is weakly associated with transcript and protein levels, independent of codon usage bias. In contrast, energetic costs explain a large proportion of variation in levels of free amino acids. In the economy of the yeast cell, there appears to be no single currency to compute the cost of amino acid synthesis, and thus a systems approach is necessary to uncover the full effects of amino acid biosynthetic cost in complex biological systems that vary with cellular and environmental conditions

Handling variability and incompleteness of biological data by flexible nets: a case study for Wilson disease.

Mathematical models that combine predictive accuracy with explanatory power are central to the progress of systems and synthetic biology, but the heterogeneity and incompleteness of biological data impede our ability to construct such models. Furthermore, the robustness displayed by many biological systems means that they have the flexibility to operate under a range of physiological conditions and this is difficult for many modeling formalisms to handle. Flexible nets (FNs) address these challenges and represent a paradigm shift in model-based analysis of biological systems. FNs can: (i) handle uncertainties, ranges and missing information in concentrations, stoichiometry, network topology, and transition rates without having to resort to statistical approaches; (ii) accommodate different types of data in a unified model that integrates various cellular mechanisms; and (iii) be employed for system optimization and model predictive control. We present FNs and illustrate their capabilities by modeling a well-established system, the dynamics of glucose consumption by a microbial population. We further demonstrate the ability of FNs to take control actions in response to genetic or metabolic perturbations. Having bench-marked the system, we then construct the first quantitative model for Wilson disease-a rare genetic disorder that impairs copper utilization in the liver. We used this model to investigate the feasibility of using vitamin E supplementation therapy for symptomatic improvement. Our results indicate that hepatocytic inflammation caused by copper accumulation was not aggravated by limitations on endogenous antioxidant supplies, which means that treating patients with antioxidants is unlikely to be effective

Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes

Background: Phosphorylation is the most frequent post-translational modification made to proteins and may regulate protein activity as either a molecular digital switch or a rheostat. Despite the cornucopia of high-throughput (HTP) phosphoproteomic data in the last decade, it remains unclear how many proteins are phosphorylated and how many phosphorylation sites (p-sites) can exist in total within a eukaryotic proteome. We present the first reliable estimates of the total number of phosphoproteins and p-sites for four eukaryotes (human, mouse, Arabidopsis, and yeast). Results: In all, 187 HTP phosphoproteomic datasets were filtered, compiled, and studied along with two low-throughput (LTP) compendia. Estimates of the number of phosphoproteins and p-sites were inferred by two methods: Capture-Recapture, and fitting the saturation curve of cumulative redundant vs. cumulative non-redundant phosphoproteins/p-sites. Estimates were also adjusted for different levels of noise within the individual datasets and other confounding factors. We estimate that in total, 13 000, 11 000, and 3000 phosphoproteins and 230 000, 156 000, and 40 000 p-sites exist in human, mouse, and yeast, respectively, whereas estimates for Arabidopsis were not as reliable. Conclusions: Most of the phosphoproteins have been discovered for human, mouse, and yeast, while the dataset for Arabidopsis is still far from complete. The datasets for p-sites are not as close to saturation as those for phosphoproteins. Integration of the LTP data suggests that current HTP phosphoproteomics appears to be capable of capturing 70% to 95% of total phosphoproteins, but only 40% to 60% of total p-sites