Urinary metabolite biomarkers of pregnancy complications associated with maternal exposure to particulate matter

Particulate matter 2.5 (PM2.5) is associated with reproductive health and adverse pregnancy outcomes. However, studies evaluating biological markers of PM2.5 are lacking, and identifying biomarkers for estimating prenatal exposure to prevent pregnancy complications is essential. Therefore, we aimed to explore urine metabolites that are easy to measure as biomarkers of exposure. In this matched case-control study based on the PM2.5 exposure, 30 high PM2.5 group (>15 μg/m3) and 30 low PM2.5 group (<15 μg/m3) were selected from air pollution on pregnancy outcome (APPO) cohort study. We used a time-weighted average model to estimate individual PM exposure, which used indoor PM2.5 and outdoor PM2.5 concentrations by atmospheric measurement network based on residential addresses. Clinical characteristics and urine samples were collected from participants during the second trimester of pregnancy. Urine metabolites were quantitatively measured using gas chromatography-mass spectrometry following multistep chemical derivatization. Statistical analyses were conducted using SPSS version 21 and MetaboAnalyst 5.0. Small for gestational age and gestational diabetes (GDM) were significantly increased in the high PM2.5 group, respectively (P = 0.042, and 0.022). Fifteen metabolites showed significant differences between the two groups (P < 0.05). Subsequent pathway enrichment revealed that four pathways, including pentose and glucuronate interconversion with three pentose sugars (ribose, arabinose, and xylose; P < 0.05). The concentration of ribose increased preterm births (PTB) and GDM (P = 0.044 and 0.049, respectively), and the arabinose concentration showed a tendency to increase in PTB (P = 0.044). Therefore, we identified urinary pentose metabolites as biomarkers of PM2.5 and confirmed the possibility of their relationship with pregnancy complications.

Metabolomic profile of seminal plasma from Guzerá bulls (Bos indicus) with contrasting sperm freezability phenotypes

The present study evaluated the seminal plasma metabolome of Bos indicus Guzerá bulls with good (n = 4) and poor (n = 5) sperm freezability. Animals were raised in natural pasture of a 'Caatinga' ecosystem, in the semi-arid region of Brazil. Seminal plasma samples were subjected to gas chromatography coupled to mass spectrometry and data, analysed using bioinformatics tools (Cytoscape with the MetScape plug-in). Sixty-two metabolites were identified in the bovine seminal plasma. Fatty acids and conjugates and organic compounds were the predominant seminal fluid metabolites, followed by carboxylic acids and derivatives, amino acids, benzenes and steroids and derivatives, carbohydrates and carbohydrate conjugates and prenol lipids. Multivariate analysis indicated a distinct separation of seminal plasma metabolomes from bulls with contrasting sperm freezability. Abundances of propanoic acid, d-ribose and glycine were greater in the seminal plasma of bulls with good sperm freezability. Heptadecanoic acid and undecanoic acid were the predominant in bulls of poor sperm freezability. Propanoic acid is an energy source for spermatozoa and may act as an antimicrobial component in semen. Glycine acts against oxidizing and denaturing reactions. d-ribose is also an energy source and reduces apoptosis and oxidative stress. Undecanoic acid may protect sperm against fungal damage. This study provides fundamental information approximately the seminal plasma metabolome of tropically adapted bulls and its association with sperm freezability. However, further studies with larger groups of animals are needed to validate those metabolites as markers of sperm freezability. This strategy could support the selection of sires with superior sperm cryoresistance.

129Xe NMR-Protein Sensor Reveals Cellular Ribose Concentration

Dysregulation of cellular ribose uptake can be indicative of metabolic abnormalities or tumorigenesis. However, analytical methods are currently limited for quantifying ribose concentration in complex biological samples. Here, we utilize the highly specific recognition of ribose by ribose-binding protein (RBP) to develop a single-protein ribose sensor detectable via a sensitive NMR technique known as hyperpolarized 129Xe chemical exchange saturation transfer (hyper-CEST). We demonstrate that RBP, with a tunable ribose-binding site and further engineered to bind xenon, enables the quantitation of ribose over a wide concentration range (nM to mM). Ribose binding induces the RBP "closed" conformation, which slows Xe exchange to a rate detectable by hyper-CEST. Such detection is remarkably specific for ribose, with the minimal background signal from endogenous sugars of similar size and structure, for example, glucose or ribose-6-phosphate. Ribose concentration was measured for mammalian cell lysate and serum, which led to estimates of low-mM ribose in a HeLa cell line. This highlights the potential for using genetically encoded periplasmic binding proteins such as RBP to measure metabolites in different biological fluids, tissues, and physiologic states.

Detecting specific saccharides via a single indicator

An improved synthesis of a rhodamine boronic acid indicator is reported. This compound is used in an optimized data collection protocol for wavelength- and time-dependent selectivity of sugars such as fructose and ribose derivatives. One indicator is thus used to selectively distinguish structurally related sugar analytes.

Genetic, hormonal, and metabolomic influences on social behavior and sex preference of XXY mice

XXY men (Klinefelter syndrome) are testosterone deficient, socially isolated, exhibit impaired gender identity, and may experience more homosexual behaviors. Here, we characterize social behaviors in a validated XXY mouse model to understand mechanisms. Sociability and gender preference were assessed by three-chambered choice tasks before and after castration and after testosterone replacement. Metabolomic activities of brain and blood were quantified through fractional synthesis rates of palmitate and ribose (GC-MS). XXY mice exhibit greater sociability than XY littermates, particularly for male mice. The differences in sociability disappear after matching androgen exposure. Intact XXY, compared with XY, mice prefer male mice odors when the alternatives are ovariectomized female mice odors, but they prefer estrous over male mice odors, suggesting that preference for male mice may be due to social, not sexual, cues. Castration followed by testosterone treatment essentially remove these preferences. Fractional synthesis rates of palmitate are higher in the hypothalamus, amygdala, and hippocampus of XXY compared with XY mice but not with ribose in these brain regions or palmitate in blood. Androgen ablation in XY mice increases fractional synthesis rates of fatty acids in the brain to levels indistinguishable from those in XXY mice. We conclude that intact XXY mice exhibit increased sociability, differences in gender preference for mice and their odors are due to social rather than sexual cues and, these differences are mostly related to androgen deficiency rather than genetics. Specific metabolic changes in brain lipids, which are also regulated by androgens, are observed in brain regions that are involved in these behaviors.

Development of inosine monophosphate and its degradation products during aging of pork of different qualities in relation to basic taste and retronasal flavor perception of the meat

Inosine monophosphate (IMP) and its degradation products, ribose and hypoxanthine, are all considered to be important constituents in meat flavor formation and development. The present study explored the fate of IMP during the aging of two qualities of pork (pH >5.7 and 5.5 < pH < 5.6) and the potential relationship between IMP, hypoxanthine, and sensory attributes of pork registered both as retronasal and basic taste responses in whole meat, meat juice, and the remaining meat residue. During aging the concentration of IMP decreased with a simultaneous increase in the concentrations of inosine, hypoxanthine, and ribose. The rates at which IMP was degraded to inosine and inosine to hypoxanthine during aging were found to be in agreement with the known rate constants of the dephosphorylation of IMP and the hydrolysis of inosine, respectively. Moreover, high-pH pork resulted in a significantly higher concentration of hypoxanthine throughout storage compared with low-pH pork due to an initially higher concentration of IMP in high-pH meat. The sensory analysis showed increasing intensity in bitterness and saltiness of pork as a function of aging, with the intensity being most pronounced in the meat juice. The increasing bitterness of the pork as a function of aging coincided with the higher content of hypoxanthine in these samples, thereby suggesting that degradation of IMP to hypoxanthine might influence pork flavor. In contrast, IMP was associated with nonaged meat and the sensory attributes meaty and brothy.

Stereochemical and regiochemical trends in the selective detection of saccharides

Several discreet sugar-boronate complexes exist in solution. This is due to the complex equilibria between isomeric species of even the simplest monosaccharides. In the current investigation, we determine the regio- and stereochemical features of the various equilibrating sugar isomers that induce signal transduction in boronic acid chemosensors such as 1 as well as 2 and 3. We present a unique example of a chemosensor (1) that is selective for ribose, adenosine, nucleotides, nucleosides, and congeners. As a result of this study, we are able to predict and achieve selective fluorescence and colorimetric responses to specific disaccharides as a consequence of their terminal sugar residue linkage patterns and configurations. We also find that the combined use of chemosensors exhibiting complementary reactivities may be used cooperatively to obtain enhanced selectivity for ribose and rare saccharides.

Mass spectrometric identification and characterization of antimony complexes with ribose-containing biomolecules and an RNA oligomer

Mass spectrometric techniques have been used to study the interaction of inorganic Sb(V) with biomolecules containing a ribose or deoxyribose moiety. Electrospray (ES) mass spectra of reaction mixtures containing inorganic Sb(V) and one of several biomolecules (adenosine, cytidine, guanosine, uridine, adenosine-5'-monophosphate, adenosine-3',5'-cyclic monophosphate, ribose, or 2'-deoxyadenosine) afforded high-mass antimony-containing ions corresponding to Sb(V)-biomolecule complexes of stoichiometry 1:1, 1:2, or 1:3. The complexes were characterized by collision-induced dissociation (CID) tandem mass spectrometry (MS) using ion-trap multistage MS. The CID results revealed that Sb(V) binds to the ribose or deoxyribose moiety. Structures are proposed for the Sb-biomolecule complexes. Analysis of the reaction mixtures by reversed-phase chromatography coupled on-line to either inductively coupled plasma (ICP) MS or ES-MS showed that in solution Sb(V) forms complexes with all the analyzed biomolecules with vicinal cis hydroxyl groups. Evidence (from size-exclusion chromatography ICP-MS and direct infusion ES-MS) of complexation of Sb(V) with an RNA oligomer, but not with a DNA oligomer, supports the suggestion that the presence of vicinal cis hydroxyl groups is critical for complexation to occur. This is the first direct evidence of complexation of Sb(V) with RNA. Results obtained by studying the effect of changing reaction conditions, i.e. pH, reaction time, and Sb/biomolecule molar ratio, on the extent of Sb-biomolecule formation suggest the reaction may be of physiological importance. Selected reaction monitoring (SRM) and precursor-ion-scanning tandem MS were investigated to determine their potential to detect trace levels of the Sb-biomolecule complexes in biological samples. Application of SRM MS-MS in combination with high-performance liquid chromatography enabled successful detection of an Sb-adenosine complex that had been spiked into a complex biological matrix (liver homogenate).

Characterization of D-ribose biosynthesis in Bacillus subtilis JY200 deficient in transketolase gene

D-Ribose is a functional five-carbon sugar, which has been used for the commercial production of riboflavin. Mechanisms of d-ribose biosynthesis from xylose were investigated in the genetically engineered Bacillus subtilis JY200 with a deficiency in transketolase. A transketolase gene (tkt) disruption cassette in plasmid pUNKC was introduced into the chromosomal tkt gene in the wild type B. subtilis 168. Analysis of culture broth by thin layer chromatography confirmed that the disruption of tkt allowed B. subtilis JY200 to produce d-ribose. In a batch culture of B. subtilis JY200, a loss of cell viability was observed after glucose depletion. Fed-batch cultivation by feeding 400 gl(-1) glucose solution as a co-substrate was carried out to supply energy to xylose metabolism and to maintain cell viability throughout cultivation. Fed-batch cultivation of B. subtilis JY200 in a complex medium containing 11 gl(-1) xylose and 5 gl(-1) glucose initially gave the best result of 10.1 gl(-1)D-ribose concentration, 0.24 gg(-1)D-ribose yield and 0.29 gl(-1)h(-1) productivity, corresponding to 40-, 5- and 12-fold increases compared with those in the batch culture. A kinetic study of D-ribose production in fed-batch cultivations of B. subtilis JY200 suggested that xylose uptake might be critical to maximize D-ribose biosynthesis from xylose.

Precursors of chicken flavor. II. Identification of key flavor precursors using sensory methods

Sensory evaluation was used to identify flavor precursors that are critical for flavor development in cooked chicken. Among the potential flavor precursors studied (thiamin, inosine 5'-monophosphate, ribose, ribose-5-phosphate, glucose, and glucose-6-phosphate), ribose appears most important for chicken aroma. An elevated concentration (added or natural) of only 2-4-fold the natural concentration gives an increase in the selected aroma and flavor attributes of cooked chicken meat. Assessment of the volatile odor compounds by gas chromatography-odor assessment and gas chromatography-mass spectrometry showed that ribose increased odors described as "roasted" and "chicken" and that the changes in odor due to additional ribose are probably caused by elevated concentrations of compounds such as 2-furanmethanethiol, 2-methyl-3-furanthiol, and 3-methylthiopropanal.

Anticancerogenic effect of a novel chiroinositol-containing polysaccharide from Bifidobacterium bifidum BGN4

Strains of bifidobacteria have many health-promotion effects. Whole cells or cytoplasm extracts of Bifidobacterium bifidum BGN4, isolated from human feces, inhibited the growth of several cancer cell lines. The polysaccharide fraction (BB-pol) extracted from B. bifidum BGN4 had a novel composition, comprising chiroinositol, rhamnose, glucose, galactose, and ribose. Three human colon cancer cell lines were treated with BB-pol: HT-29, HCT-116, and Caco-2. Trypan blue exclusion assay and BrdU incorporation assay showed that BB-pol inhibited the growth of HT-29 and HCT-116 cells but did not inhibit the growth of Caco-2 cells.

Chiral-selective aminoacylation of an RNA minihelix

Amino acids in natural proteins have a chiral, asymmetric center at the alpha carbon that is of the L-configuration. The sugar backbone of natural RNAs are also homochiral, but of the D-configuration. Because protein synthesis requires the aminoacylation of RNA, it is this step that could have provided chiral selectivity. Here we show that an RNA minihelix was aminoacylated by an aminoacyl-phosphate-D-oligonucleotide with a clear preference for L- as opposed to D-amino acids. A mirror-image RNA system showed the opposite selectivity. These results suggest the possibility that the selection of L-amino acids for proteins was determined by the stereochemistry of RNA.

Derivatization for LC-electrospray ionization-MS: a tool for improving reversed-phase separation and ESI responses of bases, ribosides, and intact nucleotides

We have developed a method for analyzing polar compounds by reversed-phase LC-ESI-MS following esterification of the analytes' free hydroxyl groups with propionyl or benzoyl acid anhydride. The method was applied to members of the plant hormone group cytokinins, which includes adenine bases, ribosides/glycosides, and nucleotides substituted at N-6 with an isoprenoid side chain, spanning a wide range of polarity. It was also used to analyze other compounds of biological importance, e.g., the nucleotides AMP, ADP, and ATP. The formation of more hydrophobic derivatives had a significant impact on two aspects of the analysis. The retention on a reversed-phase material was greatly increased without the use of any acetate/formate buffer or ion pairing reagent, and the ESI response was enhanced, due to the higher surface activities of the derivatives. Detection limits of propionylated cytokinins were in the high-attomole to low-femtomole range, an improvement by factors of 10-100 compared to previously reported figures. Using an automated SPE-based purification method, 12 endogenous cytokinins were quantified in extracts from 20- to 100-mg samples of leaves (from the plant Arabidopsis thaliana) with high accuracy and precision. Furthermore, the chromatographic properties of the benzoylated AMP, ADP, and ATP in the reversed-phase LC-MS system were much better in terms of retention, separation, and sensitivity than those of their underivatized counterparts, even without the use of any ion pairing reagent. Our data show that derivatization followed by LC-ESI-MS is an effective strategy for analyzing low molecular weight compounds, enabling compounds with a wide range of polarity to be determined in a single-injection LC-MS analysis.

Chiral Induction in a Ribose-Decorated Metallostar through Intrinsic and Interionic Diastereomeric Interactions

A ribose-functionalized bpy ligand has been prepared and shown to give modest diastereomeric excesses of Lambda-[FeL(3)](2+) complexes; interconversion of Delta and Lambda cations is relatively fast, and in CHCl(3), the favored complexes with Delta- or Lambda-TRISPHAT counterions are homochiral, (Delta(+)Delta(-)) or (Lambda(+)Lambda(-)). In the case of the Delta-TRISPHAT salt, a single diastereomer is observed (de > or = 96%).

Development of a fluorescent nanosensor for ribose

To analyze ribose uptake and metabolism in living cells, nanosensors were engineered by flanking the Escherichia coli periplasmic ribose binding protein with two green fluorescent protein variants. Following binding of ribose, fluorescence resonance energy transfer decreased with increasing ribose concentration. Five affinity mutants were generated covering binding constants between 400 nM and 11.7 mM. Analysis of nanosensor response in COS-7 cells showed that free ribose accumulates in the cell and is slowly metabolized. Inhibitor studies suggest that uptake is mediated by a monosaccharide transporter of the GLUT family, however, ribose taken up into the cell was not or only slowly released, indicating irreversibility of uptake.

Quantitative chiral analysis of sugars by electrospray ionization tandem mass spectrometry using modified amino acids as chiral reference compounds

Rapid quantitative enantiomeric analysis of mannose, glucose, galactose, and ribose is achieved using electrospray ionization and cluster ion dissociation with data analysis by the kinetic method. Several modified amino acids (N-Ac-L-Phe, N-benzoyl-L-Phe, N-t-Boc-L-Phe, N-Ac-L-Pro, N-t-Boc-L-Pro, N-Fmoc-L-Pro, N-Ac-L-Tyr, O-Me-L-Tyr) and four transition divalent metal cations (Co2+, Cu2+, Ni2+, and Zn2+) were tested to select the best system for chiral recognition and quantitation of each sugar. Quantitative determinations of the enantiomeric compositions of sugar solutions were achieved using either multiple- or two-point calibration curves; differences between the actual and experimental values were <2% enantiomeric excess (ee).

Postcolumn derivatization method for determination of reducing and phosphorylated sugars in chicken by high performance liquid chromatography

A postcolumn derivatization method is described for determination of reducing sugars and phosphorylated reducing sugars from chicken meat and other foods using high-performance liquid chromatography (HPLC). Reducing sugars are extracted with ethanol/water, separated on a Kromasil amine-bonded column by isocratic analysis using acetonitrile/water as the mobile phase, and, after postcolumn reaction with tetrazolium blue, are determined by the resulting absorbance at 550 nm. Phosphorylated sugars are first dephosphorylated using alkaline phosphatase and then determined by the same method.

Effect of lipid composition on meat-like model systems containing cysteine, ribose, and polyunsaturated fatty acids

This paper compares the volatile constituents of model systems containing the important meat aroma precursors cysteine and ribose, with and without either methyl linoleate, an n-6 fatty acid, or methyl alpha-linolenate, an n-3 acid, both of which are present in meat. Many of the volatile compounds formed from the reaction between cysteine and ribose were not formed, or formed in lower amounts, when lipid was present. This may be due to the reaction between hydrogen sulfide, formed from the breakdown of cysteine, and lipid degradation products. In addition, cysteine and ribose modified lipid oxidation pathways, so that alcohols and alkylfurans were formed rather than saturated and unsaturated aldehydes. Several volatile compounds, which have been found at elevated levels in cooked meat from animals fed supplements high in n-3 acids, were formed when methyl alpha-linolenate reacted with cysteine and ribose. The possible effects of increasing the n-3 content of meat upon flavor formation during cooking are discussed.

Characteristics of xyloglucan after attack by hydroxyl radicals

It has been proposed that plant cell-wall polysaccharides are subject in vivo to non-enzymic scission mediated by hydroxyl radicals (-*OH). In the present study, xyloglucan was subjected in vitro to partial, non-enzymic scission by treatment with ascorbate plus H(2)O(2), which together generate -*OH. The partially degraded xyloglucan appeared to contain ester bonds within the backbone, as indicated by an irreversible decrease in viscosity upon alkaline hydrolysis. Aldehyde and/or ketone groups were also introduced into the polysaccharide by -*OH-attack, as indicated by staining with aniline hydrogen-phthalate and by reaction with NaB(3)H(4). The introduction of ester and oxo groups supports the proposed sequence of reactions: (a) -*OH-mediated H-abstraction to produce a carbon-centred carbohydrate radical; (b) reaction of the latter with O(2); and (c) elimination of a hydroperoxyl radical (HO(2)*-). When the partially degraded xyloglucan was reduced with NaB(3)H(4) followed by acid hydrolysis, several 3H-aldoses were detected ([3H]galactose, [3H]xylose, [3H]glucose, [3H]ribose and probably [3H]mannose), in addition to unidentified 3H-products (probably including anhydroaldoses). 3H-Alditols were undetectable, showing that few or no conventional reducing termini were introduced. Digestion of the NaB(3)H(4)-reduced, partially degraded xyloglucan with Driselase released 25 times more [3H]Xyl-alpha-(1-->6)-Glc than Xyl-alpha-(1-->6)-[3H]Glc, suggesting that the xylose side-chains of the xyloglucan had been more heavily attacked by -*OH than the glucose residues of the backbone. The radioactive xyloglucan was readily digested by cellulase, yielding 3H-products in the hepta- to nonasaccharide range. A fingerprinting strategy for identifying -*OH-attacked xyloglucan in plant cell walls is proposed.

Identification of arsenosugars at the picogram level using nanoelectrospray quadrupole time-of-flight mass spectrometry

State-of-the-art analytical methods for arsenic speciation rely typically on the availability of standards of defined structure, limiting the applicability of such methods to the determination of known compounds. Our previous high-energy tandem mass spectrometric studies demonstrated the strength of mass spectrometry for generating structurally diagnostic ions that allow for the identification of arsenic-containing ribofuranosides (arsenosugars) without the use of standards. We now report a more widely applicable and more sensitive approach, using negative-ion nano-electrospray low-energy tandem mass spectrometry for the generation of structurally useful product ions that allow for identification of arsenosugars at the picogram level. In the negative-ion mode, numerous product ions, suitable for characterizing naturally occurring dimethylated arsenosugars, were generated in high abundance. Application of the method to an algal extract unequivocally demonstrated the presence of a single dimethylated arsenosugar. In the positive-ion mode, characteristic tandem mass spectra were obtained for four trimethylarsonioribosides, allowing their identification without the need for standards. Overall it was demonstrated that nano-ES-MS/MS techniques can be used for characterizing arsenosugars on a routine basis, a necessary requirement for assessing potential health risks associated with consuming foods containing elevated levels of arsenosugars and for improving our understanding of arsenic biochemistry.

Nocardioides pyridinolyticus sp. nov., a pyridine-degrading bacterium isolated from the oxic zone of an oil shale column

A bacterial strain which is able to degrade pyridine was previously isolated from the oxic zone of an oil shale column and described as Pimelobacter sp. strain OS4T. However, Pimelobacter species have been transferred to the genera Nocardioides and Terrabacter. Strain OS4T was identified as a member of the genus Nocardioides on the basis of chemotaxonomic analysis and phylogenetic inference based on 16S ribosomal DNA (rDNA) sequence analysis. The G+C content of strain OS4T is 72.5 mol%. The cell wall peptidoglycan contains LL-diaminopimelic acid as the diamino acid. The predominant menaquinone is MK-8(H4). The cellular fatty acid profile of strain OS4T is similar to that of the genus Nocardioides. The 16S rDNA similarity of strain OS4T with previously described Nocardioides species is 94.5% +/- 0.7%, and a phylogenetic tree based on 16S rDNA sequences revealed a distinct lineage for strain OS4T within the evolutionary radiation enclosed by the genus Nocardioides. Therefore, on the basis of our data, we propose that strain OS4T should be placed in the genus Nocardioides as a member of a new species, Nocardioides pyridinolyticus. The type strain of the new species is strain OS4 (= KCTC 0074BP).

Assessment of microwave sterilization of foods using intrinsic chemical markers

The uniformity of microwave processing was investigated by measuring the formation of intrinsic chemical markers in disc-shaped and cylindrically-shaped whey protein gel model systems. These markers are formed as a result of thermally induced reactions of sugar and protein precursors. They were measured in samples placed in a pressurizable Teflon vessel and microwave heated to different peak temperatures using different power levels. Heating uniformity was mapped by sectioning the sample and analyzing for markers. The destruction of B. stearothermophilus spores in alginate beads was correlated with marker formation. The results show that the markers can be used to assess sterility and spatial time-temperature distributions in solid food samples.

Synthesis and characterization of authentic standards for the analysis of ribofuranose-containing carbohydrates by the reductive-cleavage method

Described herein is the synthesis of all positional isomers of partially methylated and acetylated or benzoylated 1,4-anhydro-D-ribitol. The benzoates are generated simultaneously from 1,4-anhydro-D-ribitol by sequential partial methylation and benzoylation or sequential partial benzoylation and methylation. The individual isomers are obtained in pure form by high-performance liquid chromatography. Debenzoylation and acetylation provided the corresponding acetates. Reported herein are the 1H NMR spectra of the benzoates and the electron-ionization mass spectra of the acetates and the tri-O-methyl derivative and also for the acetates and the tri-O-methyl derivative, their linear temperature programmed gas-liquid chromatography retention indices on three different capillary columns.

Novel (rhamnosyl and ribosyl) and uncommon (xylosyl) monosaccharide residues are present in asparagine-linked oligosaccharides of the trypanosomatid Blastocrithidia culicis

Blastocrithidia culicis is a trypanosomatid protozoon that transfers Man6GlcNAc2 in protein N-glycosylation. Compounds containing mannosyl, xylosyl, and rhamnosyl residues were found among the endo-beta-N-acetylglucosaminidase H-sensitive oligosaccharides of whole cell glycoproteins of this parasite. The compositions of some of them were as follows: Man5GlcNAc2, Man6GlcNAc2, Rha1Man5GlcNAc2, Rha2Man6GlcNAc2, Xyl1Rha2Man6-GlcNAc2, Xyl1Rha3Man6GlcNAc2, and Xyl2Rha3Man6-GlcNAc2. On the other hand, oligosaccharides containing mannosyl, xylosyl, rhamnosyl, and ribosyl units were liberated from endo-beta-N-acetylglucosaminidase-resistant glycopeptides upon treatment with N-glycanase. This is the first report on the presence of ribosyl units in eukaryote glycoconjugates, of rhamnosyl residues in asparagine-linked oligosaccharides, and of xylosyl units in high mannose-type compounds.

Structures of the modified folates in the thermophilic archaebacteria Pyrococcus furiosus

The structures of the modified folates present in Pyrococcus furiosus have been determined. This was accomplished largely by the characterization of the arylamines resulting from the air oxidative cleavage of the reduced modified folates present in these cells, using both chemical and enzymatic methods. Cell extracts separated on DEAE-Sephadex columns showed one major peak containing the arylamines derived from the modified folates. These arylamines were not retained on the DEAE-Sephadex columns, indicating that they contained no net negative charge. Purification of the azo dye derivatives of these arylamines on a Bio-Gel P-6 column showed the presence of three different compounds (compounds 1, 2, and 3) in an average amount of 4.1, 7.6, and 22 nmol/g dry weight of cells, respectively. Each of these compounds readily underwent mild acid hydrolysis (0.1 M HCl, 110 degrees C, 1 min) to produce the azo dye derivative of 5-(p-aminophenyl)-1,2,3,4-tetrahydroxypentane (pAPT). The structure and stereochemistry (ribo) of the pAPT was the same as the pAPT present in methanopterin. In addition, compounds 1, 2, and 3 were each shown to contain 1 mol equiv of ribose and 1, 2, and 3 mol equiv of N-acetylglucosamine (gluNAc), respectively, and were designated as the azo dye derivatives of pAPT-ribose-gluNAc, pAPT-ribose-(gluNAc)2, and pAPT-ribose-(gluNAc)3. Each of these compounds was readily cleaved to the azo dye derivative of pAPT-ribose by the enzymatic action of beta-N-acetylglucosaminidase, indicating that all the gluNAc residues were beta-linked.(ABSTRACT TRUNCATED AT 250 WORDS)

Modification interference approach to detect ribose moieties important for the optimal activity of a ribozyme

A new approach for modification interference studies is presented. It involves the use of phosphorothioates as a handle to analyze any desired base or sugar modification. This method was applied to identify ribose and phosphate moieties which could be important in the pre-tRNA recognition of E. coli RNase P RNA (M1 RNA). The utility of this technique was confirmed by detecting the inhibitory effect of a deoxyribose in the 5'-flank (position-1). This site was already known to interfere with RNase P cleavage, if modified. We have analyzed pre-tRNA(Tyr) and pre-tRNA(Phe) and found different interference patterns for both tRNAs. Two unpaired regions were involved in both pre-tRNAs. Phosphorothioates interfered at the transition between acceptor- and D-arms. The results with deoxythymidines in the T-loop indicated that deoxyribose moieties or the extra methyl group in thymidine could interfere with RNAse P cleavage. These data suggest that even in complete pre-tRNAs, only a few intact ribonucleotides are important in the substrate recognition by RNase P. We have demonstrated the potential of this new approach which offers many future applications in all fields involving nucleic acids, for example RNA processing, action of ribozymes, tRNA charging and studies related to DNA promoter recognition.

Escherichia coli O9:K38 capsular antigen: another ribofuranose-containing glycan

The primary structure of the O-deacetylated acidic capsular antigen of Escherichia coli O9:K38 was shown by glycose analysis, methylation analysis, and one- and two-dimensional 1H- and 13C-n.m.r. spectroscopy to be composed of repeating linear pentasaccharide units having the structure.

Electrotransfer of [32P]NAD allows labeling of ADP-ribosylated proteins in intact Chinese hamster ovary cells

CHO-K1D cells electroporated in buffers containing [32P]NAD incorporated the label in a voltage-dependent manner. Electroporation with 650 V/cm at 1460 microF in Ham's F12 medium supplemented with 10 mM Hepes, pH 7.1, resulted in a greater than 20-fold increase in [32P]NAD uptake, while decreasing relative cellular survival by only 6%. Exposure of cells to gamma irradiation (20 Gy) prior to electroporation increased the steady-state level of poly(ADP-ribosylated) nuclear proteins two- to four-fold over that of unirradiated control cells. These data indicate that electrotransfer of [32P]NAD is a simple and rapid means of labeling the cellular NAD pool and should prove useful in the analysis of the relationship between poly(ADP-ribosylation) of nuclear proteins and DNA repair.

Separation and partial characterization of Maillard reaction products by capillary zone electrophoresis

Capillary zone electrophoresis proved useful for separating small amounts of both charged and uncharged solutes that are otherwise difficult to analyse. A typical complex mixture that had previously resisted all analytical approaches, including reversed-phase separations, is the products arising from the reaction of free amino acids with aldehydic sugars (Maillard reaction products). By using capillary zone electrophoresis [untreated capillary 50 cm x 75 microns I.D., 18 kV, 0.02 mol/l phosphate buffer (pH 7.5)], a number of products resulting from the reaction of glucose or ribose with glycine, alanine and isoleucine were separated and partially characterized. They were separated (1) without derivatization (and profiles of compounds absorbing at 220 nm were obtained), (2) as phenylthiocarbamyl derivatives in a search for reactive amino groups and (3) after derivatzation with 2,4-dinitrophenylhydrazine in a search for a method for compounds with a free aldehydic group. Phenylthiocarbamyl derivatives were separated in 0.005 mol/l borate buffer (pH 9.6) at 20 kV and 25 microA. Separation of 2,4-dinitrophenylhydrazones was effected by electrokinetic micellar chromatography in the same apparatus using a 50 cm x 75 microns I.D. capillary at 10 kV in 0.01 mol/l Na2HPO4-0.006 mol/l tetraborate, 0.050 mol/l with respect to sodium dodecyl sulphate. The results are compared with those given by high-performance liquid and thin-layer chromatography.

Effects of the O2' hydroxyl group on Z-DNA conformation: structure of Z-RNA and (araC)-[Z-DNA]

The left-handed Z structures of two hexamers [d(CG)r(CG)d(CG) and d(CG)(araC)d(GCG)] containing ribose and arabinose residues have been solved by X-ray diffraction analysis at 1.5-A resolution. Their conformations closely resemble that of the canonical Z-DNA. The O2' hydroxyl groups of both rC and araC residues form intramolecular hydrogen bonds with N2 of the 5' guanine residue and replace the bridging water molecules in the deep groove of Z-DNA, which stabilize the guanine in the syn conformation. The araC residue can be incorporated into the Z structure readily and facilitates B to Z transition, as supported by UV absorption spectroscopic studies. In contrast, in Z-RNA the ribose of the cytidine residue is twisted in order to form the respective hydrogen bond. The potential biological roles of the modified Z-DNA containing anticancer nucleoside araC and of Z-RNA are discussed.

Effect of storage on mutagenicity, absorbance and content of furfural in the ribose-lysine maillard system

The stability with time of browned mixtures characterized by different water activities (aw 0.98, 0.84 and 0.60) and heating temperatures (100, 120, 140 and 160 degrees C) was analysed using the ribose-lysine model system. The results obtained demonstrated the occurrence, during storage, of changes both in the composition of the browned mixtures and in their mutagenic properties, as detected with the Ames test. Only the browned mixtures obtained at 100 degrees C showed a progressive increase in mutagenicity during storage, matched by an increase in ultraviolet and visible light absorbance and of furfural content. In the browning mixtures characterized by a more advanced stage of the Maillard reaction, in which mutagenic activity had initially been found to be undetectable, such activity became evident during storage.

Influence of water activity and reaction temperature of ribose-lysine and glucose-lysine Maillard systems on mutagenicity, absorbance and content of furfurals

The effect of water activity (aw 0.98, 0.84 and 0.60) and reaction temperature (100, 120, 140 and 160 degrees C) on the mutagenic activity of the Maillard reaction products in heated ribose-lysine and glucose-lysine model systems, was investigated. In the ribose-lysine system, heated at 100 degrees C, the mutagenic activity of the mixture increased as the water activity was lowered. On the contrary, no dependence between mutagenic activity and water activity was observed in the glucose-lysine system. At higher temperatures, in both systems, the presence in the browned mixtures of an antibacterial activity interfering with the bacterial mutagenicity assay was observed. Under all the conditions tested, the ribose-lysine system turned out to be the most reactive by producing higher levels of mutagens. Furthermore, in this system, the antimicrobial interference was more easily detectable. In the model systems used, the browning reaction mixtures were analysed for their absorption spectrum between 200-460 nm, and for the accumulation of furfurals. The results obtained showed that, at temperatures between 120 and 140 degrees C there is a correlation among reaction temperature, absorbance at 420 and around 280 nm, mutagenic activity of the mixture and the level of furfurals. Changes in the levels of furfurals can be related to changes in mutagenicity of the browned mixtures.

Identification of poly G bound to thymidylate synthase

Thymidylate synthase activity is increased in some methotrexate-resistant strains of Streptococcus faecium. The purified enzyme is associated with a polynucleotide which is not removed by dialysis. This polynucleotide contains one mole each of purine ribose and phosphate per mole base. Phosphate analyses after incubation with digestive enzymes indicate a tetranucleotide with one terminal phosphate. The constituent nucleosides are recovered quantitatively in a specific assay for guanosine. On HPLC, they are inseparable from authentic guanosine and the UV spectrum after HPLC is identical to that of guanosine. We conclude that poly G (GpGpGpGp) is bound to thymidylate synthase.

Biosynthesis of thiamine: origin of the methyl carbon atom of the pyrimidine moiety in Salmonella typhimurium

Two biosynthetic, unevenly labeled samples of 5-aminoimidazole riboside were prepared. The incorporation of radioactivity from these labeled samples was studied in a Salmonella typhimurium strain able to use this riboside as precursor of the pyrimidine moiety of thiamine. In one sample, the ribose part was labeled almost equally at C-1' and C-2' and threefold more at C-3' but unlabeled at C-4' and C-5'. The pyrimidine moiety of thiamine derived from it was found almost inactive at C-5, C-7; the specific activity of the methyl carbon atom was found close to that of C-1' or C-2' of ribose in the precursor. On the other hand, only a poor incorporation of radioactivity occurred from a sample in which the ribose part was labeled mainly at C-1'. We conclude that C-5, C-7 of the pyrimidine moiety of thiamine derive from C-4', C-5' and the methyl carbon atom of the pyrimidine derives from C-2' of the ribose part of 5-aminoimidazole ribotide.

Structural studies on the oligosaccharide moiety of the lipopeptidophosphoglycan from Trypanosoma cruzi

The structure of the carbohydrate moiety of the lipopeptidophosphoglycan from Trypanosoma cruzi was studied by 13C NMR spectroscopy and by methylation analysis of the original and of an acid-degraded sample. An oligosaccharide, consisting of 2-O-substituted and 6-O-substituted mannoses, which is linked to the ceramide, was separated by partial acid hydrolysis from an external chain that contained 3-O-substituted mannopyranosyl residues. beta-D-Galactofuranosyl terminal units are attached to position 3 of (1----2)-linked mannopyranose. Besides the previously reported monosaccharide components (mannose, galactose, glucose and glucosamine), ribose was identified in a partial acid hydrolysate of the lipopeptidophosphoglycan. The last three sugars are minor components and their organization into the overall structure of the lipopeptidophosphoglycan has not been determined.

Absence of DNA in yolk platelets of Bufo arenarum oocytes

The absence of DNA in the yolk platelets of Bufo arenarum oocytes was verified. Oocytes from the coelomic cavity were used in order to avoid possible contamination by the ovarian tissue. Four methods for DNA analysis were employed, and the possibility of interference was carefully checked. The presence of three possible contaminants, which produced positive reactions from the DNA analysis, was detected. These were the glycosaminoglycan from the superficial layer of the platelets, sucrose, and polyvinylpyrrolidone from the buffer commonly used during the isolation of platelets. The present evidence points to the necessity of using at least two different methods for DNA determination with due regard for their sensitivity and specificity before any firm conclusion can be reached on the presence or absence of DNA in nonnuclear and mitochondrial parts of the oocyte.

Empirical 13C-n.m.r.-correlations between the Escherichia coli K 13 and LP 1092 capsular polysaccharides and model oligosaccharides containing D-ribose and 3-deoxy-D-manno-2-octulosonic acid

The proton-decoupled, Fourier-transform, 13C-n.m.r. spectra of the two anomeric sodium (methyl 3-deoxy-7-O-beta-D-ribofuranosyl-alpha- and beta-D-manno-2-octulopyranosid)onates, of the two anomeric sodium [methyl 3-deoxy-7-O-(2-O-beta-D-ribofuranosyl-beta-D-ribofuranosyl)-alpha- or -beta-D-manno-2-octulopyranosid]onates, and of methyl 2-O-beta-D-ribofuranosyl-beta-D-ribofuranoside have been recorded. The constitutions of these compounds correspond to repeating units and partial structures of the capsular polysaccharides from Escherichia coli K 13, K 20, K 23, and LP 1092 strains. The 13C-n.m.r.-line patterns of these oligosaccharide derivatives and the corresponding polysaccharides show striking differences dependent upon the anomeric configurations of the KDO residues. These differences may be used for the identification, by visual or computer-assisted pattern analysis, of the anomeric configurations of KDO-residues in oligo- or poly-saccharides. Thus, it was confirmed that the KDO residues in the K 13, K 20, and K 23 polysaccharides have the beta anomeric configuration, whereas those in the LP 1092 polysaccharide have the alpha anomeric configuration.

Conversion of D-mannitol to D-ribose: a newly discovered pathway in Escherichia coli

A mutant (mtlD) strain of Escherichia coli unable to oxidize mannitol-1-phosphate to fructose-6-phosphate was used to study the fate of mannitol-1-phosphate. D-[1-14C]mannitol entered the cells via the phosphotransferase system and was phosphorylated equally at carbon 1 or 6. The label disappeared gradually from the mannitol-1-phosphate pool, and some 60% of the 14C was recovered in nucleic acids. Ribose was isolated from the purified RNA. The 14C label distribution in the isolated ribose precluded a simple hexose-to-pentose conversion by elimination of one terminal carbon from mannitol-1-phosphate. The 14C from mannitol-1-phosphate that did not enter macromolecules was found in CO2 and in some organic, non-phosphorylated compounds that were not identified. We suggest that the de novo synthesis of mannitol-1-phosphate in E. coli may be a reaction specifically dedicated to the biosynthesis of ribose.

The distribution of monosaccharides and hexosamines in the oviduct of Salamandra salamandra (L.) (Amphibia, Urodela)

Biochemical analysis of the different segments of the oviduct in the ovoviviparous salamander, Salamandra salamandra, reveals the monosaccharides glucose, galactose, fucose, mannose, ribose and the hexosamines glucosamine and mannosamine. In segment 1 (pars recta) ribose and mannose are absent, and in segments 2 (p. convoluta I) and 5 (p. convoluta IV, uterus) mannose is not detectable; fucose is absent in the uterus. Segments 3 (p. convoluta II) and 4 (p. convoluta II) contain all sugars identified. The main hexoses present in the glandular segments are galactose, fucose and glucose.

Trimethylsilyl-sugar profiles of Streptococcus milleri and Streptococcus mitis

Seventy strains of 'viridans-group' streptococci were analysed gas chromatographically after preparation of trimethylsilyl ethers of their cellular sugars. The resulting profiles were evaluated as a possible aid to taxonomy. Glycerol, glucose, galactose, N-acetyl-glucosamine and N-acetylmuramic acid were found in all strains, in varying amounts. Rhamnose was the major neutral sugar in most strains, other than representatives of Streptococcus mitis, which invariably had ribose and usually anhydroribitol but no rhamnose. One strain of Strep. mitis possessed arabitol. Some strains of Strep. mitis and 'Strep. milleri' were alone in containing N-acetylgalactosamine. A combination of N-acetylgalactosamine and rhamnose in the absence of ribose was diagnostic for strains of 'Strep. milleri'.

Nitrogenase from the photosynthetic bacterium Rhodopseudomonas capsulata: purification and molecular properties

Nitrogenase proteins were isolated from cultures of the photosynthetic bacterium Rhodopseudomonas capsulata grown on a limiting amount of ammonia. Under these conditions, the nitrogenase N2ase A was active in vivo, and nitrogenase activity in vitro was not dependent upon manganese and the activating factor. The nitrogenase proteins were also isolated from nitrogen-limited cultures in which the in vivo nitrogenase activity had been stopped by an ammonia shock. This nitrogenase activity, N2ase R, showed an in vitro requirement for manganese and the activating factor for maximal activity. The Mo-Fe protein (dinitrogenase) was composed of two dissimilar subunits with molecular weights of 55,000 and 59,500; the Fe protein (dinitrogenase reductase), from either type of culture, was composed of a single subunit (molecular weight), 33,500). The metal and acid labile sulfur contents of both nitrogenase proteins were similar to those found for previously isolated nitrogenases. The Fe proteins from both N2ase A and N2ase R contained phosphate and ribose, 2 mol of each per mol of N2ase R Fe protein and about 1 mol of each per mol of N2ase A Fe protein. The greatest difference between the two types of Fe protein was that the N2ase R Fe protein contained about 1 mol per mol of an adenine-like molecule, whereas the N2ase A Fe protein content of this compound was insignificant. These results are compared with various models previously presented for the short-term regulation of nitrogenase activity in the photosynthetic bacteria.

Effect of 1 alpha-hydroxycholecalciferol on bone mass and composition of cortical bone in adult male rats

High daily oral doses of 10 micrograms 1 alpha-hydroxycholecalciferol (1 alpha-OHD3) administered to adult rats produced toxic effects such as loss of body weight, hypercalcemia and bone resorption. However, small (0.09 microgram) and moderate (0.9 microgram) daily doses of 1 alpha-OHD3 did not produce toxic effects during six weeks of observation. Serum calcium level was only slightly raised, but bone mass, bone mineral and organic matter contents, including collagen and nucleic acids of the cortical bone matrix, significantly increased, while the amount of glycosaminoglycans was reduced. Treatment with small daily doses of 1 alpha-OHD3 (0.09 microgram/day for six weeks) produced a more pronounced effect on the variables studied than did the moderate dosage (0.9 microgram). 1 alpha-OHD3 promotes new bone formation in the mature rat skeleton after conversion to 1,25 dihydroxycholecalciferol [1,25(OH)2D3] in the liver, probably by exerting a direct effect on bone tissue rather than through indirect hormonal events.

Conformational analysis of a modified ribotetranucleoside triphosphate: m6(2)A-U-m6(2)A-U studied in aqueous solution by nuclear magnetic resonance at 500 MHz

The complete and unequivocal assignment of the 24 ribose proton signals of m6(2)A(1)-U(2)-m6(2)(3)-U(4) by means of 500 MHz NMR spectroscopy at 17 degrees C is given. this assignment is based on scrupulous decoupling experiments carries out at various temperatures. Analysis of the observed chemical shifts and coupling constants of the tetramer shows that the two fragments -m6(2)A(3)-U(4) comprising the 3'-end occur mainly in the classical right-handed stack conformation, whereas the 5'-end the -U(2)- residue appears bulged out in favour of a less well-defined stacking interaction between the bases m6(2)A(1)-and -m6(2)A(3)-. Conformational populations about each of the torsional degrees of freedom along the backbone are discussed. A modernized version of pseudorotation analysis is used to delineate the conformational behaviour of the four ribose rings.