Randomised clinical trial: low-FODMAP rye bread vs. regular rye bread to relieve the symptoms of irritable bowel syndrome.

BACKGROUND: Grains are high in FODMAPs (Fermentable Oligo-, Di-, Monosaccharides And Polyols) and often considered as triggers of IBS symptoms. AIM: To evaluate if rye bread low in FODMAPs would be better tolerated than regular rye bread in subjects with IBS. METHODS: The study was conducted as a randomised double blind controlled cross-over study (n = 87). Participants were supplied with both regular rye bread and low-FODMAP rye bread for 4 weeks. Symptoms were measured with a symptom severity scoring system (IBS-SSS) and visual analogue scale (VAS) assessments of individual symptoms. Quality of life was monitored. Colonic fermentation was measured by the breath hydrogen test and dietary intake by food diaries. RESULTS: Dietary fibre intake increased during both study periods compared to baseline. Many signs of IBS i.e. flatulence, abdominal pain, cramps and stomach rumbling were milder on the low-FODMAP rye bread (P-values: 0.04; 0.049; 0.01 and 0.001). The mean of VAS measurements was favourable towards LF bread [-3 (95% CI): -6 to -1, P = 0.02] but no differences were detected in IBS-SSS or quality of life. The AUC of breath hydrogen values was significantly lower during the low-FODMAP bread period (median 52.9 vs. 72.6; P = 0.01). CONCLUSIONS: Low-FODMAP rye bread helps IBS patients to control their symptoms and reduces gastrointestinal gas accumulation. However, replacing regular rye bread by low-FODMAP bread without concomitant broader dietary changes does not improve quality of life or IBS-SSS. Nonetheless, inclusion of low-FODMAP rye bread in diet might be one way that IBS patients could increase their fibre intake.

Improving the performance of SOMFA by use of standard multivariate methods.

Self-Organizing Molecular Field Analysis (SOMFA) comes with a built-in regression methodology, the Self-Organizing Regression (SOR), instead of relying on external methods such as PLS. In this article we present a proof of the equivalence between SOR and SIMPLS with one principal component. Thus, the modest performance of SOMFA on complex datasets can be primarily attributed to the low performance of the SOMFA regression methodology. A multi-component extension of the original SOR methodology (MCSOR) is introduced, and the performances of SOR, MCSOR and SIMPLS are compared using several datasets. The results indicate that in general the performance of SOMFA models is greatly improved if SOR is replaced with a more sophisticated regression method. The results obtained for the Cramer (CBG) dataset further underline the fact that it is a very poor benchmark dataset and should not be used to evaluate the performance of QSAR techniques.

Synthesis and antimicrobial activity of the symmetric dimeric form of Temporin A based on 3-N,N-di(3-aminopropyl)amino propanoic acid as the branching unit.

Dimeric derivative of antimicrobial peptide amide Temporin A (TA) was synthesized by using a new branching unit 3-N,N-di(3-aminopropyl)amino propanoic acid (DAPPA), which allows building of the parallelly symmetric alpha-helical structures. Antimicrobial effect of the original peptide amide, its monomeric carboxy (TAc) and novel dimeric (TAd) analogues were tested against Staphylococcus aureus (Gram-positive) and Escherichia coli (Gram-negative). Both TA and TAd completely inhibited the growth of S. aureus at the concentrations of 5 and 10 microM, respectively, whereas TAc did not show any inhibitory activity. The activities of TAc, TA and TAd correlate directly with the net charges of the molecules, +1, +2 and +4, respectively. Interestingly, TAd displayed antibacterial effect against E. coli at a concentration of 10 microM, where as monomeric TA did not show any activity at concentration as high as 20 microM. The results indicate that the novel structural modification improves the antibacterial properties of Temporin A especially towards Gram-negative bacteria.

Effect of supplementation with organic selenium on mercury status as measured by mercury in pubic hair.

The purpose of this study was to evaluate the effect of four months of yeast-based selenium supplementation on selenium and mercury status in subjects with low serum selenium. The study was carried out in Rakvere, Estonia. Pubic hair mercury, serum selenium and blood selenium concentrations in 23 subjects (serum selenium < 90 micrograms/l) were investigated before and after selenium supplementation. Thirteen subjects were randomized into the selenium supplementation group and ten into the placebo group. The selenium supplementation group received daily 100 micrograms of selenomethionine. Selenium supplementation reduced pubic hair mercury level by 34% (p = 0.005) and elevated serum selenium by 73% and blood selenium by 59% in the supplemented group (p < 0.001 for both). The study indicates that mercury accumulation in pubic hair can be reduced by dietary supplementation with small daily amounts of organic selenium in a short range of time.

Oligonucleotides containing 9-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-adenine and -guanine: synthesis, hybridization and antisense properties.

Synthesis of 9-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-adenine (7, ara-A2'F) and -guanine (12, ara-G2'F) was accomplished via the condensation of 2,6-dichloropurine (1) with 2-deoxy-2-fluoro-1,3,5-tri-O-benzoyl-alpha-D-arabinofuranose (2) as a key chemical step. Condensation of silylated N6-benzoyladenine (6) with 2 gave, after deblocking and chromatographic separation, ara-A2'F (7) (14%), it's alpha-anomer 8 (14%) and N7-alpha-isomer 9 (25%). The PSEUROT analysis of N9-betaD-arabinosides 7 and 12 manifested slight preference for the S rotamer (64%) for the former, and an equal population of the N and S rotamers for the latter. The arabinosides 7 and 12 were used for the preparation of the respective phosphoamidite building blocks 13 and 14 for automated oligonucleotide synthesis. Four 15-mer oligonucleotides (ONs) complementary to the initiation codon region of firefly luciferase mRNA were prepared: unmodified 2'-deoxy-ON (AS 1) and containing (i) ara-A2'F instead of the only A (AS2), (ii) ara-G2'F vs. 3-G from the 5'-terminus (AS3), and (iii) both arabinosides at the same positions (AS4). All these ONs display practically the same (i) affinity to both complementary DNA and RNA, and (ii) ability to inhibit a luciferase gene expression in a cell-free transcription-translation system.

Folding of alpha(r)beta and epsilonbeta reverse turns; a nanosecond molecular dynamics simulation of the hexapeptide MSALNT and the octapeptide NMSALNTL in water.

Folding of the hexapeptide MSALNT and the octapeptide NMSALNTL were investigated using 2.8 ns molecular dynamics (MD) simulations in aqueous solution. In the simulation, the central sequence SALN of the hexapeptide folded rapidly within 200 ps into an alpha(r)beta turn conformation (type VIII conformation) and remained in this conformation for the rest of the trajectory. The sequence SALN of the octapeptide needed 2 ns to fold via epsilonbeta conformations into a similar conformation. The results join the sequences into a growing group of sequences which have a tendency to form secondary structures and thereby to direct protein folding. The structures of the reverse turn conformations were in accordance with the experimental results (Hakalehto et al., Eur J. Biochem. 250, 19-29 (1997)). The main driving force of folding seems to be the hydrophobic interaction between the side chains of Ala and Leu at the i+1 and i+2 positions of the beta-turn.

A bovine dander allergen, comparative modeling, and similarities and differences in folding with related proteins.

The most important allergenic protein in cow dander and urine is Bos d 2. It is proposed to belong to the family of lipocalins, which are proteins capable of binding small hydrophobic molecules. The allergenic properties of Bos d 2 indicate an interaction between the accessible regions of the native protein and IgE. In this work, a three-dimensional model was created for Bos d 2 by comparative modeling, and features characteristic of outlier lipocalins were observed. The protruding regions of the surface were characterized and used in predicting the possible B-cell epitopes. There is a pocket inside the core and its size is appropriate for small molecules. The model shows a hydrophilic amino acid side chain of glutamic acid 115 on the inner surface of the hole and a phenylalanine as the "gatekeeper" instead of tyrosine, which is common in experimentally modeled lipocalins.

Internal motions of native lysozyme are more organized than those of mutants: a principal component analysis of molecular dynamics data.

Principal component analysis (PCA) of molecular dynamics simulations of hen egg white lysozyme and its mutants indicate that even small changes in the amino acid sequence alter considerably the internal molecular motions and that the internal motions are more organized in the native enzyme than in the mutants.

Mercury-binding capacity of organic and inorganic selenium in rat blood and liver.

The mercury-binding capacity of seleno-DL-methionine and selenium dioxide was assessed in male Wistar rats. Mercury was supplied as fish loaves made of northern pike or rainbow trout. We used a selenium concentration of 3.4 mg/kg fish, about sixfold compared to the equivalent quantity of mercury. Seleno-DL-methionine had a tendency to increase both methyl mercury and total mercury in blood, although it also seemed to reduce the proportion of methyl mercury of total mercury. Selenium dioxide lowered mercury levels by 24-29% both in the blood and in the liver of rats that were fed with northern pike.

Metabolism of the dimethyl ester of [2,3-(13)C]succinic acid in rat hepatocytes.

Hepatocytes prepared from overnight fasted rats were incubated for 120 min in the presence of the dimethyl ester of [2,3-(13)C]succinic acid (10 mM). The identification and quantification of 13C-enriched metabolites in the incubation medium were performed by a novel computational strategy for the deconvolution of NMR spectra with multiplet structures and constraints. The generation of 13C-labelled metabolites, including succinate, fumarate, malate, lactate, alanine, aspartate and glucose accounted for about half of the initial amount of the ester present in the incubation medium. A fair correlation was observed between the experimental abundance of each 13C-labelled glucose isotopomer and the corresponding values derived from a model for the metabolism of [2,3-(13)C]succinate. Newly formed glucose was more efficiently labelled in the carbon C5 than C2, as well as the carbon C6 than C1, supporting the concept that D-glyceraldehyde-3-phosphate may undergo enzyme-to-enzyme channelling between glyceraldehyde-3-phosphate dehydrogenase and phosphofructoaldolase.

Identification of a common structural motif in the disordered N-terminal region of bacterial flagellins--evidence for a new class of fibril-forming peptides.

Flagellin proteins lacking the N- or C-terminus form polymers of reduced filament stability and straight morphology, in contrast to the coiled native flagella. In the present study, the N-terminal amino acid sequence of flagellins of the anaerobic beer spoilage bacteria Pectinatus cerevisiiphilus and Pectinatus frisingiensis as well as Enterobacter aerogenes and Pseudomonas sp. were determined. Sequence similarity was revealed between these and the N-termini of all known eubacterial flagellins. Synthetic peptides corresponding to the first 15 amino acid residues of the flagellins of Pectinatus, Campylobacter jejuni, E. aerogenes or Proteus mirabilis flagellins had a spontaneous tendency under physiological conditions to form 4-6 nm broad, 1-2 microm long fibrillar structures that had a tendency to form clusters. In contrast, the Pectinatus peptide missing residues 1-3 did not form fibrils. The peptide missing residues 13-15 formed fibrils less easily, and the peptide missing residues 11-15 formed fibrils almost without clustering. In electron micrographs, the fibrillisation of the bacterial flagellar peptides resembled that of beta-amyloid and prion peptides. 1H-NMR and infrared spectroscopy studies with homology analysis indicate that although the flagellar N-terminal peptides are flexible with many conformational minima, they have a significant tendency to form beta-type structures and a loop in the middle of the peptide. The hydrophobic character of the N-terminus together with the property of forming a conserved beta-strand-loop-beta-strand motif may be related to a mechanism involved in attaining the proper morphology and stability of the flagellar filament, by providing a device for facilitating the attachment of the flagellin monomers to each other. The flagellar peptides represent a new class of fibril-forming peptides.

A computational strategy for the deconvolution of NMR spectra with multiplet structures and constraints: analysis of overlapping 13C-2H multiplets of 13C enriched metabolites from cell suspensions incubated in deuterated media.

A computational strategy for the deconvolution of complex spectra involving scalar multiplet patterns is presented. This approach fits spectra that can be composed of single resonances as well as scalar coupling multiplets for which resonance frequencies, intensities, and lineshape parameters can be optimized. For multiplets, the coupling constant also is optimized. Any external information about the optimizable parameters can be taken into account as external constraints. A lineshape described by absorptive and dispersive Lorentzian and Gaussian contributions and the baseline with up to 40 Fourier and polynomial terms can likewise be optimized. The effectiveness of the procedure is assessed on the basis of computer simulated deconvolutions of a composite of 1J(13C-2H) multiplets arising from a mixture of all possible 13C-2H isotopomers of deuterated L-[3-13C]lactate generated from cell preparations incubated with D-[1-13C]glucose in D2O, which was analyzed previously with a manual deconvolution procedure (R. Willem, M. Biesemans, F. Kayser, W. J. Malaisse, Magn, Reson. Med. 31, 259-267 (1994)). The use of constraints is shown to lead to an improvement in the results. The fitting strategies and the importance of the baseline as an origin of bias are discussed.

Reactions of hydrated formaldehyde in nasal mucus.

Formaldehyde is a well known toxic air impurity affecting the upper respiratory tract. It rapidly forms methylene glycol in water. Reactions of the hydrated formaldehyde with nasal mucus were studied by C-13 NMR spectroscopy. In the NMR spectra methylene glycol dominated and only minor signals from possible reactions were observed. This finding suggests that nasal mucus effectively protects nasal epithelium against formaldehyde.

Substrate specificity and reaction mechanism of human glycoasparaginase. The N-glycosidic linkage of various glycoasparagines is cleaved through a reaction mechanism similar to L-asparaginase.

Human glycoasparaginase (N4-(beta-N-acetyl-D-glucosaminyl)-L-asparaginase, EC 3.5.1.26) hydrolyzes a series of compounds that contain L-asparagine residue with free alpha-amino and alpha-carboxyl groups. Substrates include high mannose and complex type glycoasparagines as well as those that lack the di-N-acetylchitobiose moiety, L-aspartic acid beta-methyl ester and L-aspartic acid beta-hydroxamate. The enzyme is inactive toward L-asparagine and L-glutamine and glycoasparagines containing substituted alpha-amino and/or alpha-carboxyl groups. In the presence of the acyl acceptor hydroxylamine, glycoasparaginase catalyzes the synthesis of L-aspartic acid beta-hydroxamate from aspartyl-glucosamine, L-aspartic acid beta-methyl ester, and L-aspartic acid. 13C NMR studies using 18O-labeled L-aspartic acid demonstrate that glycoasparaginase catalyzes an oxygen exchange between water and the carboxyl group at C-4 of L-aspartic acid. These results indicate that glycoasparaginase reacts as an exo-hydrolase toward the L-asparagine moiety of the substrates and the free alpha-amino and alpha-carboxyl groups are required for the enzyme reaction. The results are consistent with an L-asparaginase-like reaction pathway which involves a beta-aspartyl enzyme intermediate. Since glycoasparaginase is active toward a series of structurally different glycoasparagines, we suggest the revised systematic name of N4-(beta-glycosyl)-L-asparaginase for the enzyme.

Structural and electronic properties of MX compounds related to TA100 mutagenicity. A semi-empirical molecular orbital QSAR study.

The structural and electronic properties of chlorofuranones including MX and its anhydride were calculated using the semi-empirical AM1 method to elucidate the key features related to the strong mutagenic activity of MX. Significant correlations were found between Ames TA100 mutagenicity and the following electronic parameters of chlorofuranones: LUMO energy (r = 0.9607, n = 17), electron affinity (r = 0.9557), LUMO electron density at the alpha-carbon (r = 0.8855) and partial charge of the alpha-carbon (r = 0.8812). Based on these results, a molecular orbital QSAR model for the mutagenic activity of 17 MX analogues is presented. The controversial role of the open-chain tautomers of MX compounds, chlorinated butenoic acids, is discussed briefly.

About the mutagenicity of chlorine-substituted furanones and halopropenals. A QSAR study using molecular orbital indices.

Electron affinities, frontier molecular orbital energies and electron densities at individual carbon atoms were calculated for 11 chlorofuranones including the strong mutagen 3-chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone (MX) and for 5 halopropenals by semi-empirical AM1 and ab initio STO-3G methods. Significant correlations were found between Ames TA100 mutagenicity and the following AM1 electronic parameters of chlorofuranones: electron affinity (r = 0.9556). LUMO energy (r = 0.9332) and frontier electron density of LUMO at the alpha-carbon (r = 0.8882). In halopropenals only LUMO electron density at the beta-carbon correlates well with mutagenicity. The observed correlations suggest a reaction mechanism in which chlorofuranones and halopropenals act as electron acceptors in the interaction with DNA.

Kinetics of reaction of cis-diamminedichloroplatinum(II) with DNA.

A method based on cation exchange chromatography was developed to determine the adducts formed in the reaction of cis-diamminedichloroplatinum(II) (cis-Pt) with DNA. DNA was incubated with various concentrations of cis-Pt for various periods of time, ethanol precipitated, and enzymatically digested to nucleosides and Pt-containing oligonucleotides. The unmodified nucleosides were separated from the positively charged intra- and interstrand cis Pt adducts with a weak cation exchanger, CM-Sephadex C-25, and the adducts were further purified by HPLC. The main adduct was shown to be an intrastrand cross-link of cis-Pt bound to the N-7 atoms of two neighboring guanines. The minor adducts were intra- and interstrand cross-links of cis-Pt with adenine and guanine and an interstrand cross-link of cis-Pt with two guanines. At low levels of DNA-modification (cis-Pt:nucleotide = 1:50-1:1000) the intrastrand cross-link of cis-Pt with two guanines consisted of 60-70% of the total platination of DNA. At higher levels of DNA-modification (greater than 1:20), the amount of undigested products increased, indicating shielding of DNA by cis-Pt from nucleolytic enzymes.

Excretion kinetics of the DNA adducts of cis-diamminedichloroplatinum(II) formed in vitro in rat urine.

The main adduct of cis-diamminedichloroplatinum(II) (cis-Pt) with DNA, cis-[Pt(NH3)2(dGpdG)], was administered i.p. to rats. Urine was collected daily for 4 days. The adduct was purified by a weak cation exchanger and quantitated by HPLC with UV detection. The recovery of the adduct was 30.0 +/- 7.0% (mean +/- SEM). The main reason for the low recovery was the chemical instability of cis-[Pt(NH3)2 (dGpdG)] in urine as shown in an in vitro incubation. Adjusted for this instability the recovery in urine was greater than 70% of the dose. When cis-Pt-DNA (the molar ratio of cis-Pt to nucleotide = 1:50) was administered i.p. to rats only 1.25 +/- 0.23% of platinum was excreted in urine in the form of cis-[Pt(NH3)2(dGpdG)] and cis-[Pt(NH3)2(dApdG)] during the first 4 days. If the removal of the cis-Pt-DNA adducts from human tissues is to be followed, their possible slow excretion and chemical instability in urine needs to be considered.