Identification of metabolites in human hepatic bile using 800 MHz 1H NMR spectroscopy, HPLC-NMR/MS and UPLC-MS

The first application of high field NMR spectroscopy (800 MHz for 1H observation) to human hepatic bile (as opposed to gall bladder bile) is reported. The bile sample used for detailed investigation was from a donor liver with mild fat infiltration, collected during organ retrieval prior to transplantation. In addition, to focus on the detection of bile acids in particular, a bile extract was analysed by 800 MHz 1H NMR spectroscopy, HPLC-NMR/MS and UPLC-MS. In the whole bile sample, 40 compounds have been assigned with the aid of two-dimensional 1H–1H TOCSY and 1H–13C HSQC spectra. These include phosphatidylcholine, 14 amino acids, 10 organic acids, 4 carbohydrates and polyols (glucose, glucuronate, glycerol and myo-inositol), choline, phosphocholine, betaine, trimethylamine-N-oxide and other small molecules. An initial NMR-based assessment of the concentration range of some key metabolites has been made. Some observed chemical shifts differ from expected database values, probably due to a difference in bulk diamagnetic susceptibility. The NMR spectra of the whole extract gave identification of the major bile acids (cholic, deoxycholic and chenodeoxycholic), but the glycine and taurine conjugates of a given bile acid could not be distinguished. However, this was achieved by HPLC-NMR/MS, which enabled the separation and identification of ten conjugated bile acids with relative abundances varying from approximately 0.1% (taurolithocholic acid) to 34.0% (glycocholic acid), of which, only the five most abundant acids could be detected by NMR, including the isomers glycodeoxycholic acid and glycochenodeoxycholic acid, which are difficult to distinguish by conventional LC-MS analysis. In a separate experiment, the use of UPLC-MS allowed the detection and identification of 13 bile acids. This work has shown the complementary potential of NMR spectroscopy, MS and hyphenated NMR/MS for elucidating the complex metabolic profile of human hepatic bile. This will be useful baseline information in ongoing studies of liver excretory function and organ transplantation.

Combinatorial peptide ligand libraries and plant proteomics: a winning strategy at a price

The mechanism of action and properties of a solid-phase ligand library made of hexapeptides (combinatorial peptide ligand libraries or CPLL), for capturing the "hidden proteome", i.e. the low- and very low-abundance proteins constituting the vast majority of species in any proteome, as applied to plant tissues, are reviewed here. Plant tissues are notoriously recalcitrant to protein extraction and to proteome analysis. Firstly, rigid plant cell walls need to be mechanically disrupted to release the cell content and, in addition to their poor protein yield, plant tissues are rich in proteases and oxidative enzymes, contain phenolic compounds, starches, oils, pigments and secondary metabolites that massively contaminate protein extracts. In addition, complex matrices of polysaccharides, including large amount of anionic pectins, are present. All these species compete with the binding of proteins to the CPLL beads, impeding proper capture and identification / detection of low-abundance species. When properly pre-treated, plant tissue extracts are amenable to capture by the CPLL beads revealing thus many new species among them low-abundance proteins. Examples are given on the treatment of leaf proteins, of corn seed extracts and of exudate proteins (latex from Hevea brasiliensis). In all cases, the detection of unique gene products via CPLL capture is at least twice that of control, untreated sample.

Combinatorial peptide ligand libraries and plant proteomics: a winning strategy at a price

The mechanism of action and properties of a solid-phase ligand library made of hexapeptides (combinatorial peptide ligand libraries or CPLL, for capturing the "hidden proteome", i.e. the low- and very low-abundance proteins Constituting the vast majority of species in any proteome. as applied to plant tissues, are reviewed here. Plant tissues are notoriously recalcitrant to protein extraction and to proteome analysis, Firstly, rigid plant cell walls need to be mechanically disrupted to release the cell content and, in addition to their poor protein yield, plant tissues are rich in proteases and oxidative enzymes, contain phenolic Compounds, starches, oils, pigments and secondary metabolites that massively contaminate protein extracts. In addition, complex matrices of polysaccharides, including large amount of anionic pectins, are present. All these species compete with the binding of proteins to the CPLL beads, impeding proper capture and identification I detection of low-abundance species. When properly pre-treated, plant tissue extracts are amenable to capture by the CPLL beads revealing thus many new species among them low-abundance proteins. Examples are given on the treatment of leaf proteins, of corn seed extracts and of exudate proteins (latex from Hevea brasiliensis). In all cases, the detection of unique gene products via CPLL Capture is at least twice that of control, untreated sample. (c) 2008 Elsevier B.V. All rights reserved.

Effect of heat on rheology, surface hydrophobicity and molecular weight distribution of glutens extracted from flours with different bread-making quality

Gluten was extracted from flours of several different wheat varieties of varying baking quality. Creep compliance was measured at room temperature and tan 6 was measured over a range of temperatures from 25 to 95 degrees C. The extracted glutens were heat-treated for 20 min at 25, 40, 50, 60, 70 and 90 degrees C in a water bath, freeze-dried and ground to a fine powder. Tests were carried out for extractability in sodium dodecyl sulphate, free sulphydryl (SH) groups using Ellman's method, surface hydrophobicity and molecular weight (MW) distribution (MWD) using field-flow fractionation and multi-angle laser light scattering. With increasing temperature, the glutens showed a decrease in extractability, with the most rapid decreases occurring between 70 and 90 degrees C, a major transition in tan 6 at around 60 degrees C and a minor transition at 40 degrees C for most varieties, a decrease in free SH groups and surface hydrophobicity and a shift in the MWD towards higher MW. The poor bread-making variety Riband showed the highest values of tan delta and Newtonian compliance, the lowest content of free SH groups and the largest increase of HMW/LMW with increasing temperature. No significant correlations with baking volume were found between any of the measured parameters. (c) 2007 Elsevier Ltd. All rights reserved.

Oxygen isotope composition of bivalve seasonal growth increments and ambient water in the rivers Rhine and Meuse

The application of oxygen isotope ratios ({delta}18O) from freshwater bivalves as a proxy for river discharge conditions in the Rhine and Meuse rivers is investigated. We compared a dataset of water temperature and water {delta}18O values with a selection of recent shell {delta}18O records for two species of the genus Unio in order to establish: (1) whether differences between the rivers in water {delta}18O values, reflecting river discharge conditions, are recorded in unionid shells; and (2) to what extent ecological parameters influence the accuracy of bivalve shell {delta}18O values as proxies of seasonal, water oxygen isotope conditions in these rivers. The results show that shells from the two rivers differ significantly in {delta}18O values, reflecting different source waters for these two rivers. The seasonal shell {delta}18O records show truncated sinusoidal patterns with narrow peaks and wide troughs, caused by temperature fractionation and winter growth cessation. Interannual growth rate reconstructions show an ontogenetic growth rate decrease. Growth lines in the shell often, but not always, coincide with winter growth cessations in the {delta}18O record, suggesting that growth cessations in the shell {delta}18O records are a better age estimator than counting internal growth lines. Seasonal predicted and measured {delta}18O values correspond well, supporting the hypothesis that these unionids precipitate their shells in oxygen isotopic equilibrium. This means that (sub-) fossil unionids can be used to reconstruct spring-summer river discharge conditions, such as Meuse low-discharge events caused by droughts and Rhine meltwater-influx events caused by melting of snow in the Alps.

Protease-activated receptor 2 sensitizes TRPV1 by protein kinase Cepsilon- and A-dependent mechanisms in rats and mice

Proteases that are released during inflammation and injury cleave protease-activated receptor 2 (PAR2) on primary afferent neurons to cause neurogenic inflammation and hyperalgesia. PAR2-induced thermal hyperalgesia depends on sensitization of transient receptor potential vanilloid receptor 1 (TRPV1), which is gated by capsaicin, protons and noxious heat. However, the signalling mechanisms by which PAR2 sensitizes TRPV1 are not fully characterized. Using immunofluorescence and confocal microscopy, we observed that PAR2 was colocalized with protein kinase (PK) Cepsilon and PKA in a subset of dorsal root ganglia neurons in rats, and that PAR2 agonists promoted translocation of PKCepsilon and PKA catalytic subunits from the cytosol to the plasma membrane of cultured neurons and HEK 293 cells. Subcellular fractionation and Western blotting confirmed this redistribution of kinases, which is indicative of activation. Although PAR2 couples to phospholipase Cbeta, leading to stimulation of PKC, we also observed that PAR2 agonists increased cAMP generation in neurons and HEK 293 cells, which would activate PKA. PAR2 agonists enhanced capsaicin-stimulated increases in [Ca2+]i and whole-cell currents in HEK 293 cells, indicating TRPV1 sensitization. The combined intraplantar injection of non-algesic doses of PAR2 agonist and capsaicin decreased the latency of paw withdrawal to radiant heat in mice, indicative of thermal hyperalgesia. Antagonists of PKCepsilon and PKA prevented sensitization of TRPV1 Ca2+ signals and currents in HEK 293 cells, and suppressed thermal hyperalgesia in mice. Thus, PAR2 activates PKCepsilon and PKA in sensory neurons, and thereby sensitizes TRPV1 to cause thermal hyperalgesia. These mechanisms may underlie inflammatory pain, where multiple proteases are generated and released.

Natural caprine whey oligosaccharides separated by membrane technology and profile evaluation by capillary electrophoresis

The functional food market is growing rapidly and membrane processing offers several advantages over conventional methods for separation, fractionation and recovery of bioactive components. The aim of the present study was to select a process that could be implemented easily on an industrial scale for the isolation of natural lactose-derived oligosaccharides (OS) from caprine whey, enabling the development of functional foods for clinical and infant nutrition. The most efficient process was the combination of a pre-treatment to eliminate proteins and fat, using an ultrafiltration (UF) membrane of 25 kDa molecular weight cut off (MWCO), followed by a tighter UF membrane with 1 kDa MWCO. Circa 90% of the carbohydrates recovered in the final retentate were OS. Capillary electrophoresis was used to evaluate the OS profile in this retentate. The combined membrane-processing system is thus a promising technique for obtaining natural concentrated OS from whey. Powered

Conceptualising public-private partnerships: a critical appraisal of approaches to meanings and forms

Purpose – The purpose of this article is to survey various meanings attached to a public-private partnership (PPP) and related aspects in Western literature, and identify commonalities and differences between them. Additionally, the article intends to critically assess conflicting and overlapping views on contractual and institutional PPPs, their forms and models, and draw insights for transitional economies. Design/methodology/approach – The article contrasts and compares views on PPP meanings, forms and models within Western PPP literature, and also draws comparisons with understanding of partnership aspects in the Russian language sources. The article examines theories underpinning PPPs, builds connections to PPP advantages and drawbacks, and provides critical assessment of net benefits that PPPs may bring along to the society. Findings – The article concludes that future PPP research in transitional countries such as Kazakhstan and Russia, particularly in the area of organisational and power arrangements in partnerships, may delineate new concepts such as government as a guarantor of a PPP project, social significance of a PPP project, and risk management in a country's contextual environment. Practical implications – In transitional countries, in which PPPs are in their infancy, clarification of theoretical positions, and identification of commonalities and differences between meanings attached to the PPP terminology may enable better decisions by researchers and practitioners in their selection and further development of partnerships and related concepts. Originality/value – Research in the field of PPPs in transitional countries such as Russia and Kazakhstan is in its infancy. The paper intends to contribute to the body of knowledge about PPPs by providing detailed account and categorisation of their principal meanings, forms, models, underpinning theories, and drawing insights for future research in transitional countries.

The assessment of enriched apoplastic extracts using proteomic approaches

In plant tissues the extracellular environment or apoplast, incorporating the cell wall, is a highly dynamic compartment with a role in many important plant processes including defence, development, signalling and assimilate partitioning. Soluble apoplast proteins from Arabidopsis thaliana, Triticum aestivum and Oryza sativa were separated by two-dimensional electrophoresis. The molecular weights and isoelectric points for the dominant proteins were established prior to excision, sequencing and identification by matrix-assisted laser-desorption ionisation time of flight mass spectrometry (MALDI - TOF MS). From the selected spots, 23 proteins from O. sativa and 25 proteins from A. thaliana were sequenced, of which nine identifications were made in O. sativa (39%) and 14 in A. thaliana (56%). This analysis revealed that: (i) patterns of proteins revealed by two-dimensional electrophoresis were different for each species indicating that speciation could occur at the level of the apoplast, (ii) of the proteins characterised many belonged to diverse families reflecting the multiple functions of the apoplast and (iii), a large number of the apoplast proteins could not be identified indicating that the majority of extracellular proteins are yet to be assigned. The principal proteins identified in the aqueous matrix of the apoplast were involved in defence, i.e. germin-like proteins or glucanases, and cell expansion, i.e. β-D-glucan glucohydrolases. This study has demonstrated that proteomic analysis can be used to resolve the apoplastic protein complement and to identify adaptive changes induced by environmental effectors.

Effects of endogenous flour lipids on the quality of semisweet biscuits

Fractionation and reconstitution techniques were used to study the contribution of enclogenous flour lipids to the quality of semisweet (Rich Tea-type) biscuits. Biscuit flour was defatted with chloroform and baked with bakery fat but without enclogenous lipid addition. Semisweet biscuits baked from defatted flour were flatter, denser, and harder and showed collapse of gas cells during baking when compared with control biscuits. Defatted flour semisweet doughs exhibited a different rheological behavior from the control samples showing higher storage and loss moduli (G' and G" values), that is, high viscoelasticity. Functionality was restored when total nonstarch flour lipids were added back to defatted flour. Both the polar and nonpolar lipid fractions had positive effects in restoring flour quality, but the polar lipid fraction was of greatest benefit. Both fractions were needed for complete restoration of both biscuit quality and dough rheological characteristics.

Effects of endogenous flour lipids on the quality of short-dough biscuits

Fractionation and reconstitution techniques were used to study the contribution of endogenous flour lipids to the quality of short-dough (shortcake type) biscuits. Biscuit flour was defatted with chloroform and baked with bakery fat, but without endogenous lipid. Short-dough biscuits baked from defatted flour had smaller diameters, and were flatter, denser and harder than control biscuits. Defatted flour shortcake doughs exhibited different rheological behaviour from the control samples, showing higher storage and loss moduli (G' and G" values), ie higher viscoelasticity. Functionality was restored when total non-starch flour lipids were added back to defatted flour. The polar lipid fraction had a positive effect in restoring flour quality whereas the non-polar lipid fraction had no effect. Both fractions were needed for complete restoration of both biscuit quality and dough rheological characteristics. A study of the microstructure of defatted biscuits revealed that their gluten protein was more hydrated and developed than the gluten of the control biscuits. This conclusion was supported by the higher water absorption of the defatted gluten. (C) 2004 Society of Chemical Industry.

Identifying antimicrobial resistance genes of human clinical relevance within Salmonella isolated from food animals in Great Britain

To investigate the occurrence of antimicrobial resistance genes of human clinical relevance in Salmonella isolated from livestock in Great Britain. Two hundred and twenty-five Salmonella enterica isolates were characterized using an antimicrobial resistance gene chip and disc diffusion assays. Plasmid profiling, conjugation experiments and identification of Salmonella genomic island 1 (SGI1) were performed for selected isolates. Approximately 43% of Salmonella harboured single or multiple antimicrobial resistance genes with pig isolates showing the highest numbers where 96% of Salmonella Typhimurium harboured one or more resistance genes. Isolates harbouring multiple resistances divided into three groups. Group 1 isolates harboured ampicillin/streptomycin/sulphonamide/tetracycline resistance and similar phenotypes. This group contained isolates from pigs, cattle and poultry that were from several serovars including Typhimurium, 4,[5],12:i:-, Derby, Ohio and Indiana. All Group 2 isolates were from pigs and were Salmonella Typhimurium. They contained a non-sul-type class 1 integron and up to 13 transferrable resistances. All Group 3 isolates harboured a class 1 integron and were isolated from all animal species included in the study. Most isolates were Salmonella Typhimurium and harboured SGI1. Salmonella isolated from livestock was shown to harbour antimicrobial resistance genes although no or little resistance to third-generation cephalosporins or ciprofloxacin, respectively, was detected. The preponderance in pigs of multidrug-resistant Salmonella Typhimurium makes it important to introduce control measures such as improved biosecurity to ensure that they do not pass through the food chain and limit human therapeutic options.

Hypothesis management in situation assessment

A situation assessment uses reports from sensors to produce hypotheses about a situation at a level of aggregation that is of direct interest to a military commander. A low level of aggregation could mean forming tracks from reports, which is well documented in the tracking literature as track initiation and data association. In this paper there is also discussion on higher level aggregation; assessing the membership of tracks to larger groups. Ideas used in joint tracking and identification are extended, using multi-entity Bayesian networks to model a number of static variables, of which the identity of a target is one. For higher level aggregation a scheme for hypothesis management is required. It is shown how an offline clustering of vehicles can be reduced to an assignment problem.

Detection of gyrA mutations in quinolone-resistant Salmonella enterica by denaturing high-performance liquid chromatography

Denaturing high-performance liquid chromatography (DHPLC) was evaluated as a rapid screening and identification method for DNA sequence variation detection in the quinolone resistance-determining region of gyrA from Salmonella serovars. A total of 203 isolates of Salmonella were screened using this method. DHPLC analysis of 14 isolates representing each type of novel or multiple mutations and the wild type were compared with LightCycler-based PCR-gyrA hybridization mutation assay (GAMA) and single-strand conformational polymorphism (SSCP) analyses. The 14 isolates gave seven different SSCP patterns, and LightCycler detected four different mutations. DHPLC detected 11 DNA sequence variants at eight different codons, including those detected by LightCycler or SSCP. One of these mutations was silent. Five isolates contained multiple mutations, and four of these could be distinguished from the composite sequence variants by their DHPLC profile. Seven novel mutations were identified at five different loci not previously described in quinolone-resistant salmonella. DHPLC analysis proved advantageous for the detection of novel and multiple mutations. DHPLC also provides a rapid, high-throughput alternative to LightCycler and SSCP for screening frequently occurring mutations.

Use of miniaturized protein arrays for Escherichia coli O serotyping

Serological typing of Escherichia coli O antigens is a well-established method used for differentiation and identification of O serotypes commonly associated with disease. In this feasibility study, we have developed a novel somatic antibody-based miniaturized microarray chip, using 17 antisera, which can be used to detect bound whole-cell E. coli antigen with its corresponding immobilized antibody, to assess the feasibility of this approach. The chip was tested using the related 17 control strains, and the O types found by the microarray chip showed 100% correlation with the O types found by conventional typing. A blind trial was performed in which 100 E. coli isolates that had been O serotyped previously by the conventional assay were tested by the array approach. Overall, the O serotypes of 88% of isolates were correctly identified by the microarray method. For several isolates, ambiguity of O-type designation by microarray arose due to increased sensitivity of this method, allowing signal intensities of cross-reactions to be quantified. Investigation of discrepancies between conventional and microarray O serotyping indicated that some isolates upon storage had become untypeable and, therefore, gave poor signal intensity when tested by the microarray or retested by conventional means. For all 20 serotype O26 and O157 isolates, the apparent discrepancy in O serotyping was analyzed further by a third independent test, which confirmed the microarray results. Therefore, the use of miniaturized protein arrays increases the speed and efficiency of O serotyping in a cost-effective manner, and these preliminary findings suggest the microarray approach may have a higher accuracy than those of traditional O-serotyping methods.