A hierarchical Bayesian model for predicting the functional consequences of amino-acid polymorphisms

Genetic polymorphisms in deoxyribonucleic acid coding regions may have a phenotypic effect on the carrier, e.g. by influencing susceptibility to disease. Detection of deleterious mutations via association studies is hampered by the large number of candidate sites; therefore methods are needed to narrow down the search to the most promising sites. For this, a possible approach is to use structural and sequence-based information of the encoded protein to predict whether a mutation at a particular site is likely to disrupt the functionality of the protein itself. We propose a hierarchical Bayesian multivariate adaptive regression spline (BMARS) model for supervised learning in this context and assess its predictive performance by using data from mutagenesis experiments on lac repressor and lysozyme proteins. In these experiments, about 12 amino-acid substitutions were performed at each native amino-acid position and the effect on protein functionality was assessed. The training data thus consist of repeated observations at each position, which the hierarchical framework is needed to account for. The model is trained on the lac repressor data and tested on the lysozyme mutations and vice versa. In particular, we show that the hierarchical BMARS model, by allowing for the clustered nature of the data, yields lower out-of-sample misclassification rates compared with both a BMARS and a frequen-tist MARS model, a support vector machine classifier and an optimally pruned classification tree.

The anti-epileptic drug Valproic Acid (VPA) inhibits steroidogenesis in bovine theca and granulosa cells in vitro

Valproic acid (VPA) is used widely to treat epilepsy and bipolar disorder. Women undergoing VPA treatment reportedly have an increased incidence of polycystic ovarian syndrome (PCOS)-like symptoms including hyperandrogenism and oligo- or amenorrhoea. To investigate potential direct effects of VPA on ovarian steroidogenesis we used primary bovine theca (TC) and granulosa (GC) cells maintained under conditions that preserve their 'follicular' phenotype. Effects of VPA (7.8-500 µg/ml) on TC were tested with/without LH. Effects of VPA on GC were tested with/without FSH or IGF analogue. VPA reduced (P<0.0001) both basal (70% suppression; IC(50) 67±10 µg/ml) and LH-induced (93% suppression; IC(50) 58±10 µg/ml) androstenedione secretion by TC. VPA reduced CYP17A1 mRNA abundance (>99% decrease; P<0.0001) with lesser effects on LHR, STAR, CYP11A1 and HSD3B1 mRNA (<90% decrease; P<0.05). VPA only reduced TC progesterone secretion induced by the highest (luteinizing) LH dose tested; TC number was unaffected by VPA. At higher concentrations (125-500 µg/ml) VPA inhibited basal, FSH- and IGF-stimulated estradiol secretion (P<0.0001) by GC without affecting progesterone secretion or cell number. VPA reversed FSH-induced upregulation of CYP19A1 and HSD17B1 mRNA abundance (P<0.001). The potent histone deacetylase (HDAC) inhibitors trichostatin A and scriptaid also suppressed TC androstenedione secretion and granulosal cell oestrogen secretion suggesting that the action of VPA reflects its HDAC inhibitory properties. In conclusion, these findings refute the hypothesis that VPA has a direct stimulatory action on TC androgen output. On the contrary, VPA inhibits both LH-dependent androgen production and FSH/IGF-dependent estradiol production in this in vitro bovine model, likely by inhibition of HDAC.

Transient heparin-induced platelet activation linked to generation of platelet 12-lipoxygenase: findings from a randomised controlled trial

Previously we demonstrated that heparin administration during carotid endarterectomy (CEA) caused a marked, but transient increase in platelet aggregation to arachidonic acid (AA) and adenosine diphosphate (ADP), despite effective platelet cyclo-oxygenase-1 (COX-1) inhibition with aspirin. Here we investigated the metabolism of AA via platelet 12-lipoxygenase (12-LOX) as a possible mediator of the observed transient aspirin resistance, and compared the effects of unfractionated (UFH) and low-molecular-weight (LMWH) heparin. A total of 43 aspirinated patients undergoing CEA were randomised in the trial to 5,000 IU UFH (n=22) or 2,500 IU LMWH (dalteparin, n=21). Platelet aggregation to AA (4x10⁻³) and ADP (3x10⁻⁶) was determined, and the products of the COX-1 and 12-LOX pathways; thromboxane B₂ (TXB₂) and 12-hydroxyeicosatretraenoic acid (12-HETE) were measured in plasma, and in material released from aggregating platelets.Aggregation to AA increased significantly (~10-fold) following heparinisation (p<0.0001), irrespective of heparin type (p=0.33). Significant, but smaller (~2-fold) increases in aggregation to ADP were also seen, which were significantly lower in the platelets of patients randomised to LMWH (p<0.0001). Plasma levels of TxB2 did not rise following heparinisation (p=0.93), but 12-HETE increased significantly in the patients' plasma, and released from platelets stimulated in vitro withADP, with both heparin types (p<0.0001). The magnitude of aggregation to ADP correlated with 12-HETE generation (p=0.03). Heparin administration during CEA generates AA that is metabolised to 12-HETE via the 12-LOX pathway, possibly explaining the phenomenon of transient heparin-induced platelet activation. LMWH has less effect on aggregation and 12-HETE generation than UFH when the platelets are stimulated with ADP.

Characterisation of amyloid fibril formation by small heat-shock chaperone proteins human alpha A-, alpha beta- and R120G alpha B-Crystallins

alpha B-Crystallin is a ubiquitous small heat-shock protein (sHsp) renowned for its chaperone ability to prevent target protein aggregation. It is stress-inducible and its up-regulation is associated with a number of disorders, including those linked to the deposition of misfolded proteins, such as Alzheimer's and Parkinson's diseases. We have characterised the formation of amyloid fibrils by human alpha B-crystallin in detail, and also that of alpha A-crystallin and the disease-related mutant R120G (alpha B-crystallin. We find that the last 12 amino acid residues of the C-terminal region of alpha B-crystallin are predicted from their physico-chemical properties to have a very low propensity to aggregate. H-1 NMR spectroscopy reveals that this hydrophilic C-terminal region is flexible both in its solution state and in amyloid fibrils, where it protrudes from the fibrillar core. We demonstrate, in addition, that the equilibrium between different protofilament assemblies can be manipulated and controlled in vitro to select for particular alpha B-crystallin amyloid morphologies. Overall, this study suggests that there could be a fine balance in vivo between the native functional sHsp state and the formation of amyloid fibrils. (C) 2007 Elsevier Ltd. All rights reserved.

Effect of chymosin reduction and salt substitution on the properties of white salted cheese

A whey salts mixture was used as a partial substitute for sodium chloride to provide a modified Na:K ratio (1:3.4) in the manufacture of white salted cheese using ultrafiltration. Reduction of chymosin addition from 20 to 8 mu L kg(-1) of cheese was also investigated. Variation of salt and chymosin levels did not result in any significant differences in composition and physicochemical properties. The rates of proteolysis in terms of water-soluble nitrogen (WSN) and nitrogen soluble in 12% trichloroacetic acid (TCA-SN) were affected by chymosin levels but not by salt treatment. Urea-PAGE electrophoretic analysis of caseins from the cheeses manufactured using three levels of chymosin and two salt types showed that the hydrolysis of alpha(s1)-casein was higher than for beta-caseins but the differences between the cheeses were not significant (P > 0.05). The chymosin level did not have a significant effect (P > 0.05) on hardness and fracturability, suggesting that any variation in hardness due to the initial hydrolysis was being confounded by other variables. Cheeses including the whey salts product were harder and more fracturable (P < 0.01) than the cheese treated with NaCl only. Both hardness and fracturability values decreased (P < 0.05) over the maturation period. The scores for bitterness were low; neither the effects of salt nor chymosin levels were significant (P > 0.05). (c) 2005 Elsevier Ltd. All rights reserved.

Reversible thermal transition of polydiacetylene based on KTTKS collagen sequence

Here we explore the physico-chemical properties of a peptide amphiphile obtained by chemical conjugation of the collagenstimulating peptide KTTKS with 10,12-pentacosadiynoic acid which photopolymerizes as a stable and extended polydiacetylene. We investigate the self-assembly of this new polymer and rationalize its peculiar behavior in terms of a thermal conformational transition. Surprisingly, this polymer shows a thermal transition associated with a non-cooperative increase in b-sheet content at high temperature.

Incorporation of cis-9,trans-11 or trans-10,cis-12 conjugated linoleic acid into plasma and cellular lipids in healthy men

This study investigated the incorporation of cis-9,trans-11 conjugated linoleic acid (c9,t11 CLA) and trans-10,cis-12-CLA (t10,c12 CLA) into plasma and peripheral blood mononuclear cell (PBMC) lipids when consumed as supplements highly enriched in these isomers. Healthy men (n = 49, age 31 +/- 8 years) consumed one, two, and four capsules containing similar to600 mg of either c9,t11 CIA or t10,c12 CLA per capsule for sequential 8 week periods followed by a 6 week washout before consuming the alternative isomer. Both isomers were incorporated in a dosedependent manner into plasma phosphatidylcholine (PC) (c9,t11 CLA r = 0.779, t10,c12 CLA r = 0.738; P < 0.0001) and cholesteryl ester (CE) (c9,t11 CLA r = 0.706, t10,c12 CLA r = 0.788; P < 0.0001). Only t10,c12 CLA was enriched in plasma nonesterified fatty acids. Both c9,t11 CIA and t10,c12 CLA were incorporated linearly into PBMC total lipids (r = 0.285 and r = 0.273, respectively; P < 0.0005). The highest concentrations of c9,t11 CLA and t10,c12 CLA in PBMC lipids were 3- to 4-fold lower than those in plasma PC and CE. These data suggest that the level of intake is a major determinant of plasma and PBMC CLA content, although PBMCs appear to incorporate both CLA isomers less readily.

EfeUOB (YcdNOB) is a tripartite, acid-induced and CpxAR-regulated, low-pH Fe2+ transporter that is cryptic in Escherichia coli K-12 but functional in E-coli O157 : H7

Escherichia coli possesses iron transporters specific for either Fe2+ or Fe3+. Although Fe2+ is far more soluble than Fe3+, it rapidly oxidizes aerobically at pH >= 7. Thus, FeoAB, the major Fe2+ transporter of E. coli, operates anaerobically. However, Fe2+ remains stable aerobically under acidic conditions, although a low-pH Fe2+ importer has not been previously identified. Here we show that ycdNOB (efeUOB) specifies the first such transporter. efeUOB is repressed at high pH by CpxAR, and is Fe2+-Fur repressed. EfeU is homologous to the high-affinity iron permease, Ftr1p, of Saccharomyces cerevisiae and other fungi. EfeO is periplasmic with a cupredoxin N-terminal domain; EfeB is also periplasmic and is haem peroxidase-like. All three Efe proteins are required for Efe function. The efeU gene of E. coli K-12 is cryptic due to a frameshift mutation - repair of the single-base-pair deletion generates a functional EfeUOB system. In contrast, the efeUOB operon of the enterohaemorrhagic strain, O157:1147, lacks any frameshift and is functional. A 'wild-type' K-12 strain bearing a functional EfeUOB displays a major growth advantage under aerobic, low-pH, low-iron conditions when a competing metal is provided. Fe-55 transport assays confirm the ferrous iron specificity of EfeUOB.

Opposing effects of cis-9,trans-11 and trans-10,cis-12 conjugated linoleic acid on blood lipids in healthy humans

Background: Conjugated linoleic acid (CLA) is reported to have weight-reducing and antiatherogenic properties when fed to laboratory animals. However, the effects of CLA on human health and, in particular, the effects of individual CLA isomers are unclear. Objective: This study investigated the effects of 3 doses of highly enriched cis-9,trans-11 (0.59, 1.19, and 2.38 g/d) or trans-10,cis-12 (0.63, 1.26, and 2.52 g/d) CLA preparations on body composition, blood lipid profile, and markers of insulin resistance in healthy men. Design: Healthy men consumed 1, 2, and 4 capsules sequentially, containing either 80% cis-9,trans-11 CLA or 80% trans-10,cis-12 CLA for consecutive 8-wk periods. This phase was followed by a 6-wk washout and a crossover to the other isomer. Results: Body composition was not significantly affected by either isomer of CLA. Mean plasma triacylglycerol concentration was higher during supplementation with trans-10,cis-12 CLA than during that with cis-9,trans-11 CLA, although there was no influence of dose. There were significant effects of both isomer and dose on plasma total cholesterol and LDL-cholesterol concentrations but not on HDL-cholesterol concentration. The ratios of LDL to HDL cholesterol and of total to HDL cholesterol were higher during supplementation with trans-10,cis-12 CLA than during that with cis-9,trans-11 CLA. CLA supplementation had no significant effect on plasma insulin concentration, homeostasis model for insulin resistance, or revised quantitative insulin sensitivity check index. Conclusion: Divergent effects of cis-9,trans-11 CLA and trans10,cis-12 CLA appear on the blood lipid profile in healthy humans: trans-10,cis-12 CLA increases LDL:HDL cholesterol and total:HDL cholesterol, whereas cis-9,trans-11 CLA decreases them.

Effects of cis-9,trans-11 and trans-1 0,cis-12 conjugated linoleic acid on immune cell function in healthy humans

Background: Animal studies have suggested that conjugated linoleic acid (CLA), a natural component of ruminant meat and dairy products, may confer beneficial effects on health. However, little information on the effects of CLA on immune function is available, especially in humans. Furthermore, the effects of individual isomers of CLA have not been adequately investigated. Objective: This study investigated the effects of supplementing the diet with 3 doses of highly enriched cis-9,trans-11 CLA (0.59, 1.19, and 2.38 g/d) or trans-10,cis-12 CLA (0.63, 1.26, and 2.52 g/d) on immune outcomes in healthy humans. Design: The study had a randomized, double-blind, crossover design. Healthy men consumed 1, 2, and 4 capsules sequentially that contained 80% of either cis-9,trans-11 CLA or trans-10,cis-12 CLA for consecutive 8-wk periods. This regimen was followed by a 6-wk washout and a crossover to the other isomer. Results: Both CLA isomers decreased mitogen-induced T lymphocyte activation in a dose-dependent manner. There was a significant negative correlation between mitogen-induced T lymphocyte activation and the proportions of both cis-9,trans-11 CLA and trans-10,cis-12 CLA in peripheral blood mononuclear cell lipids. However, CLA did not affect lymphocyte subpopulations or serum concentrations of C-reactive protein and did not have any consistent effects on ex vivo cytokine production. Conclusion: CLA supplementation results in a dose-dependent reduction in the mitogen-induced activation of T lymphocytes. The effects of cis-9,trans-l I CLA and trans-10,cis-12 CLA were similar, and there was a negative correlation between mitogen-induced T lymphocyte activation and the cis-9,trans-11 CLA and trans-10,cis-12 CLA contents of mononuclear cells.

Incorporation of cis-9,trans-11 or trans-10,cis-12 conjugated linoleic acid into plasma and cellular lipids in healthy men

This study investigated the incorporation of cis-9,trans-11 conjugated linoleic acid (c9,t11 CLA) and trans-10,cis-12-CLA (t10,c12 CLA) into plasma and peripheral blood mononuclear cell (PBMC) lipids when consumed as supplements highly enriched in these isomers. Healthy men (n = 49, age 31 +/- 8 years) consumed one, two, and four capsules containing similar to600 mg of either c9,t11 CIA or t10,c12 CLA per capsule for sequential 8 week periods followed by a 6 week washout before consuming the alternative isomer. Both isomers were incorporated in a dosedependent manner into plasma phosphatidylcholine (PC) (c9,t11 CLA r = 0.779, t10,c12 CLA r = 0.738; P < 0.0001) and cholesteryl ester (CE) (c9,t11 CLA r = 0.706, t10,c12 CLA r = 0.788; P < 0.0001). Only t10,c12 CLA was enriched in plasma nonesterified fatty acids. Both c9,t11 CIA and t10,c12 CLA were incorporated linearly into PBMC total lipids (r = 0.285 and r = 0.273, respectively; P < 0.0005). The highest concentrations of c9,t11 CLA and t10,c12 CLA in PBMC lipids were 3- to 4-fold lower than those in plasma PC and CE. These data suggest that the level of intake is a major determinant of plasma and PBMC CLA content, although PBMCs appear to incorporate both CLA isomers less readily.

Incorporation of cis-9, trans-11 or trans-10, cis-12 conjugated linoleic acid into human erythrocytes in vivo

The purpose of this study was to determine the incorporation into erythrocytes of cis (c)-9,trans (t)-11 conjugated linoleic acid (CLA) and t10,c12 CLA consumed as supplements highly enriched in these isomers. Healthy men (31 8 years) consumed 1, 2, and 4 capsules containing approximately 80 g/100 g of either c9,t11 CLA or t10,c12 CLA for sequential 8-week periods. Fatty acid concentrations in erythrocyte total lipids were determined at baseline and after consumption of the highest dose. The increase in c9,t11 CLA concentration (0.31 g/100 g) was significantly greater than that in t10,c12 CLA (0.19 g/100 g). This was associated with minor changes in concentrations of some fatty acids of chain length greater than 20 carbons. These data suggest selective assimilation of individual CLA isomers into erythrocyte lipids and partial substitution for specific saturated and polyunsaturated fatty acids. (C) 2005 Elsevier Inc. All rights reserved.

The development and contribution of surface charge by crop residues in two Malawian acid soils

The effects of maize and soya bean residues on the pH and charge of a loamy sand (Kawalazi) and a sandy clay loam (Naming'omba) from Malawi were measured to determine both the indirect effect of the residues on soil charge through the changes in pH, and the direct contribution of charge carried on the residue surfaces. The soils had pH values (10 mM CaCl2) of 4.3 and 5.0 and organic matter contents were 1.4% and 2.7%, respectively. The clay fractions were dominated by kaolinite and goethite, and mica was present in both samples. The soils were incubated for 28 days with maize (Zea mays) and soya bean (Glycine max) residues. The maximum addition of residue (12.0%) in the Kawalazi and Naming'omba soils increased the pH from 4.3 and 5.0 to 4.8 and 5.3 (maize) and to 9.0 and 8.8 (soya bean), respectively. Negative charge increased from 2.1 and 4.7 cmol(c) kg(-1) to 3.8 and 7.5 (maize) and to 5.3 and 9.3 cmol(c) kg(-1) (soya bean). Positive charge increased from 0.72 and 0.62 to 0.87 and 0.85 cmol(c) kg(-1) (maize) and to 0.75 and 0.68 (soya bean). The charge contribution by the residues was calculated by difference between the charge on a sample incubated with residue and the charge on a soil without residue limed to the same pH value. Up to 100 cmolc negative charge and 10 cmol(c) of positive charge per kg of residue were directly contributed to the soil-residue mixture, the amounts depending on the type of residue, the extent to which the residue was decomposed in the soil and the pH of the mixture. The Anderson and Sposito method [Soil Sci. Soc. Am. J. 55 (1991) 1569] was used to partition the permanent negative charge (holding Cs+) from variable negative charge (holding Li+). In the pH range 3.7-6.5 the maize residue contributed between 3 and 26 cmol(c) of variable charge per kg of residue in the Kawalazi soil and between 6 and 25 cmol(c) per kg of residue in the Naming'omba soil. For soya bean the values were between I and 28 and between 4 and 68 cmolc per kg of residue, respectively. At a given pH value, the charge tended to increase with time of incubation and for a given addition of residue, pH decreased during incubation. Addition of residues contributed no permanent negative charge and the charge on the soil measured by Cs adsorption was independent of pH change caused by the residue showing that the method is valid for soil-residue mixtures. With time there was a decrease in the amount of permanent charge probably due to masking as humic material become adsorbed on mineral surfaces. (C) 2003 Elsevier Science B.V. All rights reserved.

Acid-base reactions between an acidic soil and plant residues

The elemental composition of residues of maize (Zea mays), sorghum (S. bicolor), groundnuts (Arachis hypogea), soya beans (Glycine max), leucaena (L. leucocephala), gliricidia (G. sepium), and sesbania (S. sesban) was determined as a basis for examining their alkalinity when incorporated into an acidic Zambian Ferralsol. Potential (ash) alkalinity, available alkalinity by titration to pH 4 and soluble alkalinity (16 It water extract titrated to pH 4) were measured. Potential alkalinity ranged from 3 73 (maize) to 1336 (groundnuts) mmol kg(-1) and was equivalent to the excess of their cation charge over inorganic anion charge. Available alkalinity was about half the potential alkalinity. Cations associated with organic anions are the source of alkalinity. About two thirds of the available alkalinity is soluble. Residue buffer curves were determined by titration with H2SO4 to pH 4. Soil buffer capacity measured by addition of NaOH was 12.9 mmol kg(-1) pH(-1). Soil and residue (10 g:0.25 g) were shaken in solution for 24 h and suspension pH values measured. Soil pH increased from 4.3 to between 4.6 (maize) and 5.2 (soyabean) and the amounts of acidity neutralized (calculated from the rise in pH and the soil buffer capacity) were between 3.9 and 11.5 mmol kg(-1), respectively. The apparent base contributions by the residues (calculated from the buffer curves and the fall in pH) ranged between 105 and 350 mmol kg(-1) of residue, equivalent to 2.6 and 8.8 mmol kg(-1) of soil, respectively. Therefore, in contact with soil acidity, more alkalinity becomes available than when in contact with H2SO4 solution. Available alkalinity (to pH 4) would be more than adequate to supply that which reacts with soil but soluble alkalinity would not. It was concluded that soil Al is able to displace cations associated with organic anions in the residues which are not displaced by H+, or that residue decomposition may have begun in the soil suspension releasing some of the non-available alkalinity. Soil and four of the residues were incubated for 100 days and changes in pH, NH4+ and NO3- concentrations measured. An acidity budget equated neutralized soil acidity with residue alkalinity and base or acid produced by N transformations. Most of the potential alkalinity of soyabean and leucaena had reacted after 14 days, but this only occurred after 100 days for gliricidia, and for maize only the available alkalinity reacted. For gliricidia and leucaena, residue alkalinity was primarily used to react with acidity produced by nitrification. Thus, the ability of residues to ameliorate acidity depends not only on their available and potential alkalinity but also on their potential to release mineral N. (C) 2004 Elsevier B.V. All rights reserved.

Effects of chlorogenic acid and bovine serum albumin on the oxidative stability of low density lipoproteins in vitro

The ability of chlorogenic acid to inhibit oxidation of human low-density lipoprotein (LDL) was studied by in vitro copper-induced LDL oxidation. The effect of chlorogenic acid on the lag time before LDL oxidation increased in a dose dependent manner by up to 176% of the control value when added at concentrations of 0.25 -1.0 μM. Dose dependent increases in lag time of LDL oxidation were also observed, but at much higher concentrations, when chlorogenic acid was incubated with LDL (up to 29.7% increase in lag phase for 10 μM chlorogenic acid) or plasma (up to 16.6% increase in lag phase for 200 μM chlorogenic acid) prior to isolation of LDL, and this indicated that chlorogenic acid was able to bind, at least weakly, to LDL. Bovine serum albumin (BSA) increased the oxidative stability of LDL in the presence of chlorogenic acid. Fluorescence spectroscopy showed that chlorogenic acid binds to BSA with a binding constant of 3.88 x 104 M-1. BSA increased the antioxidant effect of chlorogenic acid, and this was attributed to copper ions binding to BSA, thereby reducing the amount of copper available for inducing lipid peroxidation.