Nutrient sensing and signalling in plants: Potassium and phosphorus

Potassium and phosphorus are important macronutrients for crops but are often deficient in the field. Very little is known about how plants sense fluctuations in K and P and how information about K and P availability is integrated at the whole plant level into physiological and metabolic adaptations. This chapter reviews recent advances in discovering molecular responses of plants to K and P deficiency by microarray experiments. These studies provide us not only with a comprehensive picture of adaptive mechanisms, but also with a large number of transcriptional markers that can be used to identify upstream components of K and P signalling pathways. On the basis of the available information we discuss putative receptors and signals involved in the sensing and integration of K and P status both at the cellular and at the whole plant level. These involve membrane potential, voltage-dependent ion channels, intracellular Ca and pH, and transcription factors, as well as hormones and metabolites for systemic signalling. Genetic screens of reporter lines for transcriptional markers and metabolome analysis of K- and P-deficient plants are likely to further advance our knowledge in this area in the near future.

Precision placement of fertiliser for optimising the early nutrition of vegetable crops: a review of the implications for the yield and quality of crops, and their nutrient use efficiency

The research outlined in this paper highlights the importance of the early nutrition of vegetable crops, and its long-term effects on their subsequent growth and development. Results are also presented to demonstrate how the nutrient supply during the establishment stages of young seedlings and transplants can be enhanced by targeting fertiliser to a zone close to their developing roots. Three different precision fertiliser placement techniques are compared for this purpose: starter, band or side-injected fertiliser. The use of each of these methods consistently produced the same (or greater) yields at lower application rates than those from conventional broadcast applications, increasing the apparent recovery of N, P and K, and the overall efficiency of nutrient use, while reducing the levels of residual nutrients in the soil. Starter fertilisers also advanced the maturity of some crops, and enhanced produce quality by increasing the proportions of the larger and/or more desirable marketable grades. The benefits of the different placement techniques are illustrated with selected examples from research at Warwick HRI using different vegetable crops, including lettuce, onion and carrot.

How do plants respond to nutrient shortage by biomass allocation?

Plants constantly sense the changes in their environment; when mineral elements are scarce, they often allocate a greater proportion of their biomass to the root system. This acclimatory response is a consequence of metabolic changes in the shoot and an adjustment of carbohydrate transport to the root. It has long been known that deficiencies of essential macronutrients (nitrogen, phosphorus, potassium and magnesium) result in an accumulation of carbohydrates in leaves and roots, and modify the shoot-to-root biomass ratio. Here, we present an update on the effects of mineral deficiencies on the expression of genes involved in primary metabolism in the shoot, the evidence for increased carbohydrate concentrations and altered biomass allocation between shoot and root, and the consequences of these changes on the growth and morphology of the plant root system.

A benchmark-driven modelling approach for evaluating deployment choices on a multicore architecture

The complexity of current and emerging high performance architectures provides users with options about how best to use the available resources, but makes predicting performance challenging. In this work a benchmark-driven performance modelling approach is outlined that is appro- priate for modern multicore architectures. The approach is demonstrated by constructing a model of a simple shallow water code on a Cray XE6 system, from application-specific benchmarks that illustrate precisely how architectural char- acteristics impact performance. The model is found to recre- ate observed scaling behaviour up to 16K cores, and used to predict optimal rank-core affinity strategies, exemplifying the type of problem such a model can be used for.

Eddy-driven exchange between the open ocean and a sub-ice shelf cavity

The exchange between the open ocean and sub-ice shelf cavities is important to both water mass transformations and ice shelf melting. Here we use a high-resolution (500 m) numerical model to investigate to which degree eddies produced by frontal instability at the edge of a polynya are capable of transporting dense High Salinity Shelf Water (HSSW) underneath an ice shelf. The applied surface buoyancy flux and ice shelf geometry is based on Ronne Ice Shelf in the southern Weddell Sea, an area of intense wintertime sea ice production where a flow of HSSW into the cavity has been observed. Results show that eddies are able to enter the cavity at the southwestern corner of the polynya where an anticyclonic rim current intersects the ice shelf front. The size and time scale of simulated eddies are in agreement with observations close to the Ronne Ice Front. The properties and strength of the inflow are sensitive to the prescribed total ice production, flushing the ice shelf cavity at a rate of 0.2–0.4 × 106 m3 s−1 depending on polynya size and magnitude of surface buoyancy flux. Eddy-driven HSSW transport into the cavity is reduced by about 50% if the model grid resolution is decreased to 2-5 km and eddies are not properly resolved.

Influence of SNPs in nutrient-sensitive candidate genes and gene–diet interactions on blood lipids: the DiOGenes study

Blood lipid response to a given dietary intervention could be determined by the effect of diet, gene variants or gene–diet interactions. The objective of the present study was to investigate whether variants in presumed nutrient-sensitive genes involved in lipid metabolism modified lipid profile after weight loss and in response to a given diet, among overweight European adults participating in the Diet Obesity and Genes study. By multiple linear regressions, 240 SNPs in twenty-four candidate genes were investigated for SNP main and SNP–diet interaction effects on total cholesterol, LDL-cholesterol, HDL-cholesterol and TAG after an 8-week low-energy diet (only main effect), and a 6-month ad libitum weight maintenance diet, with different contents of dietary protein or glycaemic index. After adjusting for multiple testing, a SNP–dietary protein interaction effect on TAG was identified for lipin 1 (LPIN1) rs4315495, with a decrease in TAG of − 0·26 mmol/l per A-allele/protein unit (95 % CI − 0·38, − 0·14, P= 0·000043). In conclusion, we investigated SNP–diet interactions for blood lipid profiles for 240 SNPs in twenty-four candidate genes, selected for their involvement in lipid metabolism pathways, and identified one significant interaction between LPIN1 rs4315495 and dietary protein for TAG concentration.

Analyses of single nucleotide polymorphisms in selected nutrient-sensitive genes in weight-regain prevention: the DIOGENES study

BACKGROUND: Differences in the interindividual response to dietary intervention could be modified by genetic variation in nutrient-sensitive genes. OBJECTIVE: This study examined single nucleotide polymorphisms (SNPs) in presumed nutrient-sensitive candidate genes for obesity and obesity-related diseases for main and dietary interaction effects on weight, waist circumference, and fat mass regain over 6 mo. DESIGN: In total, 742 participants who had lost ≥ 8% of their initial body weight were randomly assigned to follow 1 of 5 different ad libitum diets with different glycemic indexes and contents of dietary protein. The SNP main and SNP-diet interaction effects were analyzed by using linear regression models, corrected for multiple testing by using Bonferroni correction and evaluated by using quantile-quantile (Q-Q) plots. RESULTS: After correction for multiple testing, none of the SNPs were significantly associated with weight, waist circumference, or fat mass regain. Q-Q plots showed that ALOX5AP rs4769873 showed a higher observed than predicted P value for the association with less waist circumference regain over 6 mo (-3.1 cm/allele; 95% CI: -4.6, -1.6; P/Bonferroni-corrected P = 0.000039/0.076), independently of diet. Additional associations were identified by using Q-Q plots for SNPs in ALOX5AP, TNF, and KCNJ11 for main effects; in LPL and TUB for glycemic index interaction effects on waist circumference regain; in GHRL, CCK, MLXIPL, and LEPR on weight; in PPARC1A, PCK2, ALOX5AP, PYY, and ADRB3 on waist circumference; and in PPARD, FABP1, PLAUR, and LPIN1 on fat mass regain for dietary protein interaction. CONCLUSION: The observed effects of SNP-diet interactions on weight, waist, and fat mass regain suggest that genetic variation in nutrient-sensitive genes can modify the response to diet. This trial was registered at clinicaltrials.gov as NCT00390637.

Generation of a buoyancy-driven coastal current by an Antarctic Polynya

Descent and spreading of high salinity water generated by salt rejection during sea ice formation in an Antarctic coastal polynya is studied using a hydrostatic, primitive equation three-dimensional ocean model called the Proudman Oceanographic Laboratory Coastal Ocean Modeling System (POLCOMS). The shape of the polynya is assumed to be a rectangle 100 km long and 30 km wide, and the salinity flux into the polynya at its surface is constant. The model has been run at high horizontal spatial resolution (500 m), and numerical simulations reveal a buoyancy-driven coastal current. The coastal current is a robust feature and appears in a range of simulations designed to investigate the influence of a sloping bottom, variable bottom drag, variable vertical turbulent diffusivities, higher salinity flux, and an offshore position of the polynya. It is shown that bottom drag is the main factor determining the current width. This coastal current has not been produced with other numerical models of polynyas, which may be because these models were run at coarser resolutions. The coastal current becomes unstable upstream of its front when the polynya is adjacent to the coast. When the polynya is situated offshore, an unstable current is produced from its outset owing to the capture of cyclonic eddies. The effect of a coastal protrusion and a canyon on the current motion is investigated. In particular, due to the convex shape of the coastal protrusion, the current sheds a dipolar eddy.

Experimentally driven atomistic model of 1,2 Polybutadiene

We present an efficient method of combining wide angle neutron scattering data with detailed atomistic models, allowing us to perform a quantitative and qualitative mapping of the organisation of the chain conformation in both glass and liquid phases. The structural refinement method presented in this work is based on the exploitation of the intrachain features of the diffraction pattern and its intimate linkage with atomistic models by the use of internal coordinates for bond lengths, valence angles and torsion rotations. Atomic connectivity is defined through these coordinates that are in turn assigned by pre-defined probability distributions, thus allowing for the models in question to be built stochastically. Incremental variation of these coordinates allows for the construction of models that minimise the differences between the observed and calculated structure factors. We present a series of neutron scattering data of 1,2 polybutadiene at the region 120-400K. Analysis of the experimental data yield bond lengths for C-C and C=C of 1.54Å and 1.35Å respectively. Valence angles of the backbone were found to be at 112° and the torsion distributions are characterised by five rotational states, a three-fold trans-skew± for the backbone and gauche± for the vinyl group. Rotational states of the vinyl group were found to be equally populated, indicating a largely atactic chan. The two backbone torsion angles exhibit different behaviour with respect to temperature of their trans population, with one of them adopting an almost all trans sequence. Consequently the resulting configuration leads to a rather persistent chain, something indicated by the value of the characteristic ratio extrapolated from the model. We compare our results with theoretical predictions, computer simulations, RIS models and previously reported experimental results.

Climate-driven spatial mismatches between British orchards and their pollinators: increased risks of pollination deficits

Understanding how climate change can affect crop-pollinator systems helps predict potential geographical mismatches between a crop and its pollinators, and therefore identify areas vulnerable to loss of pollination services. We examined the distribution of orchard species (apples, pears, plums and other top fruits) and their pollinators in Great Britain, for present and future climatic conditions projected for 2050 under the SRES A1B Emissions Scenario. We used a relative index of pollinator availability as a proxy for pollination service. At present there is a large spatial overlap between orchards and their pollinators, but predictions for 2050 revealed that the most suitable areas for orchards corresponded to low pollinator availability. However, we found that pollinator availability may persist in areas currently used for fruit production, but which are predicted to provide sub-optimal environmental suitability for orchard species in the future. Our results may be used to identify mitigation options to safeguard orchard production against the risk of pollination failure in Great Britain over the next 50 years; for instance choosing fruit tree varieties that are adapted to future climatic conditions, or boosting wild pollinators through improving landscape resources. Our approach can be readily applied to other regions and crop systems, and expanded to include different climatic scenarios.

The effect of macro and micro-nutrient fortification of biscuits on their sensory properties and on hedonic liking of older people

BACKGROUND: Under-nutrition in older adults is widespread. Oral nutritional supplement beverages (ONS) are prescribed, yet consumption by older people is often insufficient. A variety of supplement formats may improve nutrient intake. This study developed protein and micro-nutrient fortified biscuits and evaluated their sensory attributes and liking by older people. Two micro-nutrient strategies were taken, to match typical ONS and to customise to the needs of older people. RESULTS: Oat biscuits and gluten-free biscuits developed contained over 12% protein and over 460 kcal 100 g-1 . Two small (40 g) biscuits developed to match ONS provided approximately 40% of an ONS portion of micro-nutrients and 60% of macro-nutrients; however, the portion size was considered realistic whereas the average ONS portion (200 mL) is excessive. Biscuits developed to the needs of older adults provided, on average, 18% of the reference nutrient intake of targeted micro-nutrients. Sensory characteristics were similar between biscuits with and without micro-nutrient fortification, leading to no differences in liking. Fortified oat biscuits were less liked than commercial oat biscuits, partly attributed to flavour imparted by whey protein fortification. CONCLUSION: Macro- and micro-nutrient fortification of biscuits could provide an alternative fortified snack to help alleviate malnutrition in older adults.

Supporting visual assessment of food and nutrient intake in a clinical care setting

Monitoring nutritional intake is an important aspect of the care of older people, particularly for those at risk of malnutrition. Current practice for monitoring food intake relies on hand written food charts that have several inadequacies. We describe the design and validation of a tool for computer-assisted visual assessment of patient food and nutrient intake. To estimate food consumption, the application compares the pixels the user rubbed out against predefined graphical masks. Weight of food consumed is calculated as a percentage of pixels rubbed out against pixels in the mask. Results suggest that the application may be a useful tool for the conservative assessment of nutritional intake in hospitals.

Data-driven treatment selection for seamless phase II/III trials incorporating early-outcome data

Seamless phase II/III clinical trials are conducted in two stages with treatment selection at the first stage. In the first stage, patients are randomized to a control or one of k > 1 experimental treatments. At the end of this stage, interim data are analysed, and a decision is made concerning which experimental treatment should continue to the second stage. If the primary endpoint is observable only after some period of follow-up, at the interim analysis data may be available on some early outcome on a larger number of patients than those for whom the primary endpoint is available. These early endpoint data can thus be used for treatment selection. For two previously proposed approaches, the power has been shown to be greater for one or other method depending on the true treatment effects and correlations. We propose a new approach that builds on the previously proposed approaches and uses data available at the interim analysis to estimate these parameters and then, on the basis of these estimates, chooses the treatment selection method with the highest probability of correctly selecting the most effective treatment. This method is shown to perform well compared with the two previously described methods for a wide range of true parameter values. In most cases, the performance of the new method is either similar to or, in some cases, better than either of the two previously proposed methods.

An interdisciplinary modelling approach asessing the cost-effectiveness of agri-environmental measures on reducing nutrient concentration to WFD thresholds under climate change: the case of the Louros catchment

The application of the Water Framework Directive (WFD) in the European Union (EU) targets certain threshold levels for the concentration of various nutrients, nitrogen and phosphorous being the most important. In the EU, agri-environmental measures constitute a significant component of Pillar 2—Rural Development Policies in both financial and regulatory terms. Environmental measures also are linked to Pillar 1 payments through cross-compliance and the greening proposals. This paper drawing from work carried out in the REFRESH FP7 project aims to show how an INtegrated CAtchment model of plant/soil system dynamics and instream biogeochemical and hydrological dynamics can be used to assess the cost-effectiveness of agri-environmental measures in relation to nutrient concentration targets set by the WFD, especially in the presence of important habitats. We present the procedures (methodological steps, challenges and problems) for assessing the cost-effectiveness of agri-environmental measures at the baseline situation, and climate and land use change scenarios. Furthermore, we present results of an application of this methodology to the Louros watershed in Greece and discuss the likely uses and future extensions of the modelling approach. Finally, we attempt to reveal the importance of this methodology for designing and incorporating alternative environmental practices in Pillar 1 and 2 measures.

Changes in the distribution of red foxes (Vulpes vulpes) in urban areas in Great Britain: findings and limitations of a media-driven nationwide survey

Urbanization is one of the major forms of habitat alteration occurring at the present time. Although this is typically deleterious to biodiversity, some species flourish within these human-modified landscapes, potentially leading to negative and/or positive interactions between people and wildlife. Hence, up-to-date assessment of urban wildlife populations is important for developing appropriate management strategies. Surveying urban wildlife is limited by land partition and private ownership, rendering many common survey techniques difficult. Garnering public involvement is one solution, but this method is constrained by the inherent biases of non-standardised survey effort associated with voluntary participation. We used a television-led media approach to solicit national participation in an online sightings survey to investigate changes in the distribution of urban foxes in Great Britain and to explore relationships between urban features and fox occurrence and sightings density. Our results show that media-based approaches can generate a large national database on the current distribution of a recognisable species. Fox distribution in England and Wales has changed markedly within the last 25 years, with sightings submitted from 91% of urban areas previously predicted to support few or no foxes. Data were highly skewed with 90% of urban areas having <30 fox sightings per 1000 people km-2. The extent of total urban area was the only variable with a significant impact on both fox occurrence and sightings density in urban areas; longitude and percentage of public green urban space were respectively, significantly positively and negatively associated with sightings density only. Latitude, and distance to nearest neighbouring conurbation had no impact on either occurrence or sightings density. Given the limitations associated with this method, further investigations are needed to determine the association between sightings density and actual fox density, and variability of fox density within and between urban areas in Britain.