Modelling cereal root systems for water and nitrogen capture: Towards an economic optimum

A quantitative model of wheat root systems is developed that links the size and distribution of the root system to the capture of water and nitrogen (which are assumed to be evenly distributed with depth) during grain filling, and allows estimates of the economic consequences of this capture to be assessed. A particular feature of the model is its use of summarizing concepts, and reliance on only the minimum number of parameters (each with a clear biological meaning). The model is then used to provide an economic sensitivity analysis of possible target characteristics for manipulating root systems. These characteristics were: root distribution with depth, proportional dry matter partitioning to roots, resource capture coefficients, shoot dry weight at anthesis, specific root weight and water use efficiency. From the current estimates of parameters it is concluded that a larger investment by the crop in fine roots at depth in the soil, and less proliferation of roots in surface layers, would improve yields by accessing extra resources. The economic return on investment in roots for water capture was twice that of the same amount invested for nitrogen capture. (C) 2003 Annals of Botany Company.

Characterisation of an s-type low molecular weight glutenin subunit of wheat and its proline and glutamine-rich repetitive domain

The low molecular weight glutenin subunits (LMW-GS) are major components of the glutenin polymers which determine the elastomeric properties of wheat (Triticum aestivum L.) gluten and dough. They comprise a complex mixture of components and have proved to be difficult to purify for detailed characterisation. The mature LMW subunit proteins comprise two structural domains, with one domain consisting of repeated sequences based on short peptide motifs. DNA sequences encoding this domain and a whole subunit were expressed in Escherichia coli and the recombinant proteins purified. Detailed comparisons by spectroscopy (CD, FT-IR) and dynamic light scattering indicated that the repetitive and non-repetitive domains of the proteins formed different structures with the former having an extended conformation with an equilibrium between poly-L-proline II-like structure and type II’ b-turns, and the latter a more compact globular structure rich in a-helix. Although the structures of these two domains appear to form independently, dynamic light scattering of the whole subunit dissolved in trifluoroethanol(TFE) suggested that they interact, leading to a more compact conformation. These observations may have relevance to the role of the LMW-GS in gluten structure and functionality.

Dietary supplements of whole linseed and vitamin E to increase levels of alpha-linolenic acid and vitamin E in bovine milk

The potential to increase the concentrations of n-3 polyunsaturated fatty acids (PUFAs) in milk fat was investigated by studying the effects of feeding a xylose-treated, whole cracked linseed supplement ( rich in alpha-linolenic acid) to dairy cows. Also the effect of increasing the dietary intake of vitamin E on the vitamin E status of milk was investigated. The effect of pasteurisation on milk fatty acid composition was also examined. Using a 3 x 2 factorial design, a total of 60 Holstein dairy cows were fed a total mixed ration based on grass silage supplemented with one of three levels of whole cracked linseed (78, 142 or 209 g . kg(-1) diet dry matter (DM); designated LL, ML or HL, respectively) in combination with one of two levels of additional dietary vitamin E intake ( 6 or 12 g vitamin E . animal(-1) . day(-1); designated LE or HE, respectively). Increasing lipid supplementation reduced (P < 0.01) diet DM intake and milk yield, and increased (P < 0.001) the overall content of oleic, vaccenic, alpha-linolenic and conjugated linoleic acids, and total PUFAs and monounsaturated fatty acids (MUFA). Myristic and palmitic acids in milk fat were reduced ( P < 0.001) through increased lipid supplementation. While α-linolenic acid concentrations were substantially increased this acid only accounted for 0.02 of total fatty acids in milk at the highest level of supplementation (630 g α-linolenic acid &BULL; animal(-1) &BULL; day(-1) for HL). Conjugated linoleic acid concentrations in milk fat were almost doubled by increasing the level of lipid supplementation (8.9, 10.4 and 16.1 g &BULL; kg(-1) fatty acids for LL, ML and HL, respectively). Although milk vitamin E contents were generally increased there was no benefit (P > 0.05) of increasing vitamin E intake from 6 to 12 g . animal(-1) . day(-1). The fatty acid composition of milk was generally not affected by pasteurisation.

Whole crop cereals 2. Prediction of apparent digestibility and energy value from in vitro digestion techniques and near infrared reflectance spectroscopy and of chemical composition by near infrared reflectance spectroscopy

Samples of whole crop wheat (WCW, n = 134) and whole crop barley (WCB, n = 16) were collected from commercial farms in the UK over a 2-year period (2003/2004 and 2004/2005). Near infrared reflectance spectroscopy (NIRS) was compared with laboratory and in vitro digestibility measures to predict digestible organic matter in the dry matter (DOMD) and metabolisable energy (ME) contents measured in vivo using sheep. Spectral models using the mean spectra of two scans were compared with those using individual spectra (duplicate spectra). Overall NIRS accurately predicted the concentration of chemical components in whole crop cereals apart from crude protein. ammonia-nitrogen, water-soluble carbohydrates, fermentation acids and solubility values. In addition. the spectral models had higher prediction power for in vivo DOMD and ME than chemical components or in vitro digestion methods. Overall there Was a benefit from the use of duplicate spectra rather than mean spectra and this was especially so for predicting in vivo DOMD and ME where the sample population size was smaller. The spectral models derived deal equally well with WCW and WCB and Would he of considerable practical value allowing rapid determination of nutritive value of these forages before their use in diets of productive animals. (C) 2008 Elsevier B.V. All rights reserved.

Enhancement of oleic acid and vitamin E concentrations of bovine milk using dietary supplements of whole rapeseed and vitamin E

With the aim of reducing the degree of saturation and increasing the C18:1 cis fatty acid content of milk fat, the effects of feeding high levels of whole cracked rapeseed to dairy cows was investigated together with the effect of increasing dietary intake of vitamin E on the vitamin E content of milk. Using a 3 x 3 factorial design, 90 Holstein dairy cows were fed one of three levels of whole cracked rapeseed (0 (ZR), 134 (MR) and 270 g . kg(-1) diet dry matter (DM) (HR)) in combination with one of three intakes of supplementary vitamin E (0 (ZE), 2 (ME) and 4 g . cow(-1) . d(-1) (HE)). Supplementing with up to almost 2 kg . d(-1) of rapeseed oil (diet HR) significantly (P < 0.001) increased C18: 1cis in milk fat, from 181 (ZR) to over 400 g &BULL; kg(-1) (HR) of total milk fatty acids. Concentrations of C18: 0, C18: 2 and C18: 3 fatty acids were also increased ( P < 0.001) but by a much lesser degree, and the saturated fatty acids C4: 0 to C16: 0 decreased substantially. Vitamin E supplementation increased ( P < 0.01) milk vitamin E concentrations from 1.29 (ZE) to 1.68 mg &BULL; kg(-1) whole milk (HE). Thus substantial changes in milk fat composition with potentially beneficial effects on human health were achieved and without any adverse effects on milk taste. However, these improvements must be offset against the substantial reductions ( P < 0.001) observed in voluntary feed DM consumption (ZR, 20.6; HR, 15.2 kg DM . d(-1)), milk yield (ZR, 22.9; HR, 13.2 kg . d(-1)) and milk fat concentration (ZR, 42.1; HR, 33.4 g . kg(-1)) which would not be commercially sustainable unless a considerable premium was paid for this modified milk. It seems likely that the optimum dose of dietary rapeseed is lower than used in this study.

Effect of replacing calcium salts of palm oil distillate with rapeseed oil, milled or whole rapeseeds on milk fatty-acid composition in cows fed maize silage-based diets

Inclusion of rapeseed feeds in dairy cow diets has the potential to reduce milk fat saturated fatty acid (SFA) and increase cis-monounsaturated fatty acid (cis-MUFA) content but effectiveness may depend on the form in which the rapeseed is presented. Four mid-lactation Holstein dairy cows were allocated to four maize silage-based dietary treatments according to a 4 x 4 Latin Square design, with 28-day experimental periods. Treatments consisted of a control diet (C containing 49 g/kg dry matter (DM) of calcium salts of palm oil distillate (CPO), or 49 g/kg DM of oil supplied as whole rapeseeds (WR), rapeseeds milled with wheat (MR) or rapeseed oil (RO). Replacing CPO with rapeseed feeds had no effect (P > 0.05) on milk fat and protein content, while milk yields were higher (P < 0.05) for RO and MR compared with WR (37.1, 38.1 and 34.3 kg/day, respectively). Substituting CPO with RO or MR reduced (P < 0.05) milk fat total SFA content (69.6, 55.6, 71.7 and 61.5 g/100g fatty acids for C, RO, WR and MR, respectively) and enhanced (P < 0.05) milk cis-9 18:1 MUFA concentrations (corresponding values 18.6, 24.3, 17.0 and 23.0 g/100g fatty acids) compared with C and WR. Treatments RO and MR also increased (P < 0.05) milk trans-MUFA content (4.4, 6.8, 10.5 g/100g fatty acids, C MR and RO, respectively). A lack of significant changes in milk fat composition when replacing CPO with WR suggests limited bioavailability of fatty acids in intact rapeseeds. In conclusion, replacing a commercial palm oil-based fat supplement in the diet with milled rapeseeds or rapeseed oil represented an effective strategy to alter milk fatty acid composition with the potential to improve human health. Inclusion of processed rapeseeds offered a good compromise for reducing milk SFA and increasing cis-MUFA, whilst minimising milk trans-MUFA and negative effects on animal performance.

Modelling simultaneously water content and dry matter dynamics of wheat grains

A model was devised to describe simultaneously the grain masses of water and dry matter against thermal time during grain filling and maturation of winter wheat. The model accounted for a linear increase in water mass of duration anthesis-m(1) (end of rapid water assimilation phase) and rate a, followed by a more stable water mass until in,, after which water mass declined rapidly at rate e. Grain dry matter was described as a linear increase of rate bgf until a maximum size (maxgf) was attained at m(2).The model was fitted to plot data from weekly samples of grains taken from replicated field experiments investigating effects of grain position (apical or medial), fungicide (five contrasting treatments), sowing date (early or late), cultivar (Malacca or Shamrock) and season (2001/2002 and 2002/2003) on grain filling. The model accounted for between 83 and 99% of the variation ( 2) when fitted to data from individual plots, and between 97 and 99% when fitted to treatment means. Endosperm cell number of grains from early-sown plots in the first season were also counted. Differences in maxgf between grain positions and also between cultivars were mostly the result of effects on bgf and were empirically associated with water mass at nil. Fungicide application controlled S. tritici and powdery mildew infection, delayed flag leaf senescence, increased water mass at m(1) (wm(1)), and also increased m(2), bgf and maxgf. Fungicide effects on water mass were detected before fungicide effects on dry matter, but comparison of the effects of individual fungicide treatments showed no evidence that effects on wm(1), nor on endosperm cell numbers at about m(1), were required for fungicide effects on maxgf, (c) 2005 Elsevier B.V. All rights reserved.

Action following the discovery of a global association between the whole genome and adverse event risk in a clinical drug-development programme

Observation of adverse drug reactions during drug development can cause closure of the whole programme. However, if association between the genotype and the risk of an adverse event is discovered, then it might suffice to exclude patients of certain genotypes from future recruitment. Various sequential and non-sequential procedures are available to identify an association between the whole genome, or at least a portion of it, and the incidence of adverse events. In this paper we start with a suspected association between the genotype and the risk of an adverse event and suppose that the genetic subgroups with elevated risk can be identified. Our focus is determination of whether the patients identified as being at risk should be excluded from further studies of the drug. We propose using a utility function to? determine the appropriate action, taking into account the relative costs of suffering an adverse reaction and of failing to alleviate the patient's disease. Two illustrative examples are presented, one comparing patients who suffer from an adverse event with contemporary patients who do not, and the other making use of a reference control group. We also illustrate two classification methods, LASSO and CART, for identifying patients at risk, but we stress that any appropriate classification method could be used in conjunction with the proposed utility function. Our emphasis is on determining the action to take rather than on providing definitive evidence of an association. Copyright (C) 2008 John Wiley & Sons, Ltd.

Assembly rules for protein networks derived from phylogenetic-statistical analysis of whole genomes

Background: We report an analysis of a protein network of functionally linked proteins, identified from a phylogenetic statistical analysis of complete eukaryotic genomes. Phylogenetic methods identify pairs of proteins that co-evolve on a phylogenetic tree, and have been shown to have a high probability of correctly identifying known functional links. Results: The eukaryotic correlated evolution network we derive displays the familiar power law scaling of connectivity. We introduce the use of explicit phylogenetic methods to reconstruct the ancestral presence or absence of proteins at the interior nodes of a phylogeny of eukaryote species. We find that the connectivity distribution of proteins at the point they arise on the tree and join the network follows a power law, as does the connectivity distribution of proteins at the time they are lost from the network. Proteins resident in the network acquire connections over time, but we find no evidence that 'preferential attachment' - the phenomenon of newly acquired connections in the network being more likely to be made to proteins with large numbers of connections - influences the network structure. We derive a 'variable rate of attachment' model in which proteins vary in their propensity to form network interactions independently of how many connections they have or of the total number of connections in the network, and show how this model can produce apparent power-law scaling without preferential attachment. Conclusion: A few simple rules can explain the topological structure and evolutionary changes to protein-interaction networks: most change is concentrated in satellite proteins of low connectivity and small phenotypic effect, and proteins differ in their propensity to form attachments. Given these rules of assembly, power law scaled networks naturally emerge from simple principles of selection, yielding protein interaction networks that retain a high-degree of robustness on short time scales and evolvability on longer evolutionary time scales.

Predicting functional gene links from phylogenetic-statistical analyses of whole genomes

An important element of the developing field of proteomics is to understand protein-protein interactions and other functional links amongst genes. Across-species correlation methods for detecting functional links work on the premise that functionally linked proteins will tend to show a common pattern of presence and absence across a range of genomes. We describe a maximum likelihood statistical model for predicting functional gene linkages. The method detects independent instances of the correlated gain or loss of pairs of proteins on phylogenetic trees, reducing the high rates of false positives observed in conventional across-species methods that do not explicitly incorporate a phylogeny. We show, in a dataset of 10,551 protein pairs, that the phylogenetic method improves by up to 35% on across-species analyses at identifying known functionally linked proteins. The method shows that protein pairs with at least two to three correlated events of gain or loss are almost certainly functionally linked. Contingent evolution, in which one gene's presence or absence depends upon the presence of another, can also be detected phylogenetically, and may identify genes whose functional significance depends upon its interaction with other genes. Incorporating phylogenetic information improves the prediction of functional linkages. The improvement derives from having a lower rate of false positives and from detecting trends that across-species analyses miss. Phylogenetic methods can easily be incorporated into the screening of large-scale bioinformatics datasets to identify sets of protein links and to characterise gene networks.