Whole crop cereals 1. Effect of method of harvest and preservation on chemical composition, apparent digestibility and energy value

A total of 133 samples (53 fermented unprocessed, 19 fermented processed. 62 urea-treated processed) of whole crop wheat (WCW) and 16 samples (five fermented unprocessed, six fermented processed, five urea-treated processed) of whole crop barley (WCB) were collected from commercial farms over two consecutive years (2003/2004 and 2004/2005). Disruption of the maize grains to increase starch availability was achieved at the point of harvest by processors fitted to the forage harvesters. All samples were subjected to laboratory analysis whilst 50 of the samples (24 front Year 1, 26 front Year 2 all WCW except four WCB in Year 2) were subjected to in vivo digestibility and energy value measurements using mature wether sheep. Urea-treated WCW had higher (P<0.05) pH, and dry matter (DM) and crude protein contents and lower concentrations of fermentation products than fermented WCW. Starch was generally lower in fermented, unprocessed WCW and no effect of crop maturity at harvest (as indicated by DM content) on starch concentrations was seen. Urea-treated WCW had higher (P<0.05) in vivo digestible organic matter contents in the DM (DOMD) in Year 1 although this was not recorded in Year 2. There was a close relationship between the digestibility values of organic matter and gross energy thus aiding the use of DOMD to predict metabolisable energy (ME) content. A wide range of ME values was observed (WCW. 8.7-11.8 MJ/kg DM; WCB 7.9-11.2 MJ/kg DM) with the overall ME/DOMD ratio (ME = 0.0156 DOMD) in line With Studies in other forages. There was no evidence that a separate ME/DOMD relationship was needed for WCB which is helpful for practical application. This ratio and other parameters were affected by year of harvest (P<0.05) highlighting the influence of environmental and Other undefined factors. The variability in the composition and nutritive value of WCW and WCB highlights the need for reliable and accurate evaluation methods to be available to assess the Value of these forages before they are included in diets for dairy cows. (C) 2008 Elsevier B.V. All rights reserved.

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.

Validation of a FFQ for estimating whole-grain cereal food intake

Estimation of whole-grain (WG) food intake in epidemiological and nutritional studies is normally based on general diet FFQ, which are not designed to specifically capture WG intake. To estimate WG cereal intake, we developed a forty-three-item FFQ focused on cereal product intake over the past month. We validated this questionnaire against a 3-d-weighed food record (3DWFR) in thirty-one subjects living in the French-speaking part of Switzerland (nineteen female and twelve male). Subjects completed the FFQ on day 1 (FFQ1), the 3DWFR between days 2 and 13 and the FFQ again on day 14 (FFQ2). The subjects provided a fasting blood sample within 1 week of FFQ2. Total cereal intake, total WG intake, intake of individual cereals, intake of different groups of cereal products and alkylresorcinol (AR) intake were calculated from both FFQ and the 3DWFR. Plasma AR, possible biomarkers for WG wheat and rye intake were also analysed. The total WG intake for the 3DWFR, FFQ1, FFQ2 was 26 (sd 22), 28 (sd 25) and 21 (sd 16) g/d, respectively. Mean plasma AR concentration was 55.8 (sd 26.8) nmol/l. FFQ1, FFQ2 and plasma AR were correlated with the 3DWFR (r 0.72, 0.81 and 0.57, respectively). Adjustment for age, sex, BMI and total energy intake did not affect the results. This FFQ appears to give a rapid and adequate estimate of WG cereal intake in free-living subjects.

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.

Self-organisation in the assembly of gels from mixtures of different dendritic peptide building blocks

This paper investigates dendritic peptides capable of assembling into nanostructured gels, and explores the effect on self-assembly of mixing different molecular building blocks. Thermal measurements, small angle Xray scattering (SAXS) and circular dichroism (CD) spectroscopy are used to probe these materials on macroscopic, nanoscopic and molecular length scales. The results from these investigations demonstrate that in this case, systems with different "size" and "chirality" factors can self-organise, whilst systems with different "shape" factors cannot. The "size" and "chirality" factors are directly connected with the molecular information programmed into the dendritic peptides, whilst the shape factor depends on the group linking these peptides together-this is consistent with molecular recognition hydrogen bond pathways between the peptidic building blocks controlling the ability of these systems to self-recognise. These results demonstrate that mixtures of relatively complex peptides, with only subtle differences on the molecular scale, can self-organise into nanoscale structures, an important step in the spontaneous assembly of ordered systems from complex mixtures.

Reliability in the whole life cycle of building systems

Purpose – The purpose of this research is to show that reliability analysis and its implementation will lead to an improved whole life performance of the building systems, and hence their life cycle costs (LCC). Design/methodology/approach – This paper analyses reliability impacts on the whole life cycle of building systems, and reviews the up-to-date approaches adopted in UK construction, based on questionnaires designed to investigate the use of reliability within the industry. Findings – Approaches to reliability design and maintainability design have been introduced from the operating environment level, system structural level and component level, and a scheduled maintenance logic tree is modified based on the model developed by Pride. Different stages of the whole life cycle of building services systems, reliability-associated factors should be considered to ensure the system's whole life performance. It is suggested that data analysis should be applied in reliability design, maintainability design, and maintenance policy development. Originality/value – The paper presents important factors in different stages of the whole life cycle of the systems, and reliability and maintainability design approaches which can be helpful for building services system designers. The survey from the questionnaires provides the designers with understanding of key impacting factors.

Synthesis of prebiotic galactooligosaccharides using whole cells of a novel strain, Bifidobacterium bifidum NCIMB 41171

A novel strain of Bifidobacterium bifidum NCIMB 41171, isolated from a faecal sample from a healthy human volunteer and able to express beta-galactosidase activity, was used in synthesis reactions for the production of galactooligosaccharide from lactose. The beta-galactosidase activity of whole bifidobacterial cells showed an optimum activity at pH 6.8-7.0 and 40 degrees C. The transgalactosylation activity of the B. bifidum cells from 50% (w/w) lactose resulted in a galactooligosaccharide mixture (20% w/w) comprising (w/w): 25% disaccharides, 35% trisaccharides, 25% tetrasaccharides and 15% pentasaccharides. Using different initial lactose concentrations, the conversion rate to galactooligosaccharides was maximum (35%) when 55% (w/w) lactose was used. In fermentation experiments, B. bifidum showed an increased preference towards the produced galactooligosaccharide mixture, displaying higher growth rate and short-chain fatty acid production when compared with commercially available oligosaccharides.