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PubMed2006

Photocatalytic degradation of phenyl-urea herbicides chlortoluron and chloroxuron: characterization of the by-products by liquid chromatography coupled to electrospray ionization tandem mass spectrometry.

The first stages of the photocatalytic degradation of the compounds chlortoluron [3-(3-chloro-4-methylphenyl)-1,1-dimethylurea] and chloroxuron [3-[4-(4-chlorophenoxy)phenyl]-1,1-dimethylurea], belonging to the class of phenyl-urea herbicides, were investigated using high-performance liquid chromatography (HPLC) coupled to electrospray ionization ion trap tandem mass spectrometry (ESI-IT-MS/MS). Degradation was accomplished under solar radiation, using TiO2 embedded into a polyvinylidene fluoride (PVDF) transparent matrix as a heterogeneous photocatalyst. Aliquots of the chlorinated herbicide solutions were withdrawn at different times and subjected to gradient elution, reversed-phase HPLC separations, specifically optimized to obtain the highest resolution between peaks related to the herbicide degradation by-products. The latter were then investigated using MS detection; in particular, MS/MS measurements were made and structural information was obtained from the interpretation of fragmentation data. Several by-products were identified; the most important ones are hydroxylated compounds arising from the interaction between the two chlorinated herbicides and OH radicals generated at the TiO2 surface under irradiation. Other by-products were generated by slightly different processes, namely demethylation, dearylation and dechlorination, eventually followed by interaction with OH radicals.

Catalysis↗

PubMed2006

Effect of thermal processing on the flavonols rutin and quercetin.

The current research involves the study of the thermal treatment of quercetin and rutin in an aqueous model system (cooking). These substances were heated and their degradation was followed by high-performance liquid chromatography/diode-array detection (HPLC/DAD). The influence of pH and the involvement of oxygen in the degradation were studied. HPLC/electrospray ionization multi-stage mass spectrometry (ESI-MS(n)) was used for the structural characterization of the compounds produced. The influence of the degradation of the phenolic compounds on their antioxidant properties was elucidated by a electron spin resonance (ESR) spectrometry study of the reaction samples mixed with the stabilized radical, Fremy's salt. Strong degradation of the model substances took place under weak basic and oxidative conditions. Quercetin showed the most intense degradation. Protocatechuic acid could be identified as a cleavage reaction product by analyzing its retention time and molar mass during the degradation of quercetin. The structure of a second cleavage product could be identified on the basis of ESI-MS(n) fragmentation data. Also, several structures for reaction products of oxidized quercetin are suggested. The ESR analysis showed a decrease in the antioxidant activity of the reaction samples after heat treatment in aqueous solution.

Chromatography, High Pressure Liquid↗

PubMed2001

SPME-MS-MVA as a rapid technique for assessing oxidation off-flavors in foods.

A new technique using solid-phase microextraction, mass spectrometry, and multivariate analysis (SPME-MS-MVA) was developed for the study of oxidized off-flavors in foods. The analytical column of a GC-MS system was replaced with a 1-m deactivated fused-silica column, which served as a transfer line to deliver volatiles extracted from samples with a Carboxen/PDMS SPME fiber to the mass spectrometer. Mass fragmentation data resulting from the unresolved food volatile components were subjected to MVA. The mass intensities from m/z 50 to m/z 150 were selected to perform MVA. Principal component analysis based on SPME-MS-MVA provided rapid differentiation of the following types of samples: control soybean oil from soybean oil exposed to fluorescent light for various time periods; control nondairy coffee creamer from complaint ("oxidized") nondairy coffee creamer samples; fresh boiled beef from boiled beef with various levels of warmed-over flavor (WOF); and control 2% milk samples from 2% milk samples abused by light or copper exposure. SPME-MS-MVA is rapid and offers significant advantages over commercial electronic nose instruments currently being used as quality assurance tools to differentiate normal tasting food and beverage samples and ingredients from those containing off-flavors and malodors.

Animals↗

PubMed1994

Nucleotide divergence between populations of trembling aspen (Populus tremuloides) estimated with RAPDs.

In the present study, a total of 142 trees sampled from five populations of trembling aspen (Populus tremuloides Michx.) in Alberta was analyzed by the polymerase chain reaction (PCR) with five random oligonucleotide primers. Null-allele frequencies of 28 putative RAPD loci were estimated using the given departure from Hardy-Weinberg equilibrium (F1S) previously estimated with isozyme markers for the same population. Nucleotide divergence between populations was then estimated in a fashion similar to restriction-fragment data, but considering the dominance of the RAPDs. The average of nucleotide divergence between populations was in the order of 0.0005 and nucleotide divergence were found to be highly correlated with geographic distance. The results suggest that isolation by distance may be an important factor in the genetic differentiation of trembling aspen.

Alberta↗

PubMed1997

Glycoproteins in prokaryotes.

Rather recently it has become clear that prokaryotes (Archaea and Bacteria) are able to glycosylate proteins. A literature survey revealed the different types of glycoproteins. They include mainly surface layer (S-layer) proteins, flagellins, and polysaccharide-degrading enzymes. Only in a few cases is structural information available. Many different structures have been observed that display much more variation than that observed in eukaryotes. A few studies have given evidence for the function of the prokaryotic glycoprotein glycans. Also from the biosynthetic point of view, information is rather scarce. Due to their different cell structure, prokaryotes have to use mechanisms different from those found in eukaryotes to glycosylate proteins. However, from the fragmented data available for the prokaryotic glycoproteins, similarities with the eukaryotic system can be noticed.

Archaea↗

PubMed2002

On-line analysis of the (13)CO(2) labeling of leaf isoprene suggests multiple subcellular origins of isoprene precursors.

Isoprene (2-methyl-1,3-butadiene) is the most abundant biogenic hydrocarbon released from vegetation, and there is continuing interest in understanding its biosynthesis from photosynthetic precursors in leaf chloroplasts. We used on-line proton-transfer-reaction mass spectrometry (PTR-MS) to observe the kinetics of (13)C-labeling of isoprene following exposure to (13)CO(2) and then the loss of (13)C after a return to normal (12)CO(2) in oak ( Quercus agrifolia Nee) and cottonwood (Populus deltoides Barr.) leaves. Assignments of labeled isoprene species were verified by gas chromatography-mass spectrometry. For the first time, it was possible to observe the half-lives of individually (13)C-labeled isoprene species during these transitions, and to trace some of the label to a C3 fragment that contained the two isoprene carbons derived from pyruvate via the deoxyxylulose-5-phosphate (DOXP) pathway. At steady state (under (13)CO(2)), approximately 80% of isoprene carbon was labeled, with fully labeled isoprene as the major species (approx. 60%). The source of the unlabeled C is suggested to be extrachloroplastic, but not from photorespiratory carbon. After a transfer to (12)CO(2), (13)C-labeling persisted in one isoprene carbon for several hours; this persistence was much more pronounced in (i) leaves inhibited by fosmidomycin, a specific inhibitor of the DOXP pathway, and (ii) in sun leaves which have higher ratios of soluble sugars to starch. From the mass 41-44 fragment data, and labeling predicted from the DOXP pathway in chloroplasts, precursors may arise from cytosolic pyruvate/phospho enolpyruvate equivalents transported into the chloroplast; this idea was supported by an indirect measure of pyruvate labeling. Other sources of cytosolic isoprene precursors (i.e. dimethylallyl diphosphate or pentose phosphate) could not be excluded. The data obtained shed light on the half-lives of photosynthetic metabolites, exchanges of carbon between cellular pools, and suggest multiple origins of isoprene precursors in leaves.

Algorithms↗

PubMed1998

Apoptotic and non-apoptotic cell death in hormone-dependent glands.

The proliferation of cells and cell death are involved in the maintenance of appropriate tissue homeostasis. In the present study, two different mechanisms of cell death were identified in the prostate and pituitary glands when morphological data, fragmentation of DNA, and TUNEL labelling of apoptotic nuclei were compared. Typical cell death by apoptosis was identified by morphological and molecular approaches in the prostate after orchidectomy. By contrast, neither DNA fragmentation nor TUNEL labelling were found in dead cells occurring in the pituitary gland after interruption of lactation. Regressing lactotrophs were characterised by condensation and disruption of the cytoplasmic matrix, but preserved intact nuclei until advanced stages of regression. Degenerating "dark" cells comparable to those described in the pituitary were also seen coexisting with typical apoptosis in the prostate epithelial lining of orchidectomised rats. Both forms of cell death could be clearly differentiated, because dark cells suffer severe alterations of cytoplasmic organelles while maintaining the integrity of the nucleus. In contrast, apoptotic cells present well-preserved cytoplasmic organelles, but grossly disrupted nuclei with fragmentation and condensation of chromatin.

Animals↗

PubMed1992

Inhibitors of sterol synthesis. Chemical syntheses and spectral properties of 26-oxygenated derivatives of 3 beta-hydroxy-5 alpha-cholest-8(14)-en-15-one and their effects on 3-hydroxy-3-methylglutaryl coenzyme A reductase activity in CHO-K1 cells.

26-Oxygenated derivatives of delta 8(14)-15-ketosterols have been synthesized from (25R)-3 beta,26-diacetoxy-5 alpha-cholest-8(14)-en-15-one (IX) as part of a program to prepare potential metabolites and analogs of 3 beta-hydroxy-5 alpha-cholest-8(14)-en-15-one (I), a potent regulator of cholesterol metabolism. Partial hydrolysis of IX gave a mixture, from which the 3 beta,26-diol II and the 26-acetate (XI) and 3 beta-acetate (X) monoesters were isolated. Mitsunobu reaction of XI followed by hydrolysis gave (25R)-3 alpha,26-dihydroxy-5 alpha-cholest-8(14)-en-15-one (VI). Oxidation of XI with pyridinium chlorochromate followed by hydrolysis of the acetate gave (25R)-26-hydroxy-5 alpha-cholest-8(14)-ene-3,15-dione (VII). Oxidation of X with Jones reagent followed by hydrolysis of the acetate gave (25R)-3 beta-hydroxy-15-keto-5 alpha-cholest-8(14)-en-26-oic acid (IVa). Jones oxidation of II gave (25R)-3,15-diketo-5 alpha-cholest-8(14)-en-26-oic acid (VII). 1H and 13C nuclear magnetic resonance assignments and analyses of mass spectral fragmentation data are presented for each of the new compounds and their derivatives. The 3,15-diketone VII was found to be highly active in lowering the levels of 3-hydroxy-3-methylglutaryl coenzyme A reductase activity in CHO-K1 cells, with a potency comparable to that of I. In contrast, 3 alpha,26-diol VI was less potent than I or VII. The two carboxylic acid analogs IVa and VIII were considerably less potent than VI in lowering the levels of HMG-CoA reductase activity.

Animals↗

PubMed1983

The complexity of the overlap method for sequencing biopolymers.

The problem of trying to reconstruct the sequence of a biopolymer by using overlapping fragments obtained from cleaving agents is shown to be computationally intractable. This strongly suggests that any computer program for overlap sequencing, even though it may work well for a limited number of inputs, will not work sufficiently for all inputs. However, if the problem is restricted so that certain crucial fragments are known, called prime strings, a sequence can be found efficiently in all cases. Graph theory techniques for doing so can also be used to count the number of sequences consistent with the fragment data to determine whether a unique sequence has been obtained.

Amino Acid Sequence↗

PubMed2004

Towards a reference map of Eimeria tenella sporozoite proteins by two-dimensional electrophoresis and mass spectrometry.

Eimeria tenella is a parasite of great importance as a disease causing agent in the poultry industry. Until recently, biological studies have focused on specific proteins, some of which play an important role in the parasite life cycle. Post-genomic studies will make it possible to understand the complexity of the parasites and their interactions with host cells. Here we present a systematic reference map of the proteins from E. tenella sporozoites. The proteins expressed at the sporozoite stage were resolved between isoelectric points 3-10 and 4-7. They were systematically identified using mass spectrometry and 16 known Eimeria sporozoite proteins were identified on two-dimensional maps. Peptide fragmentation data from mass spectrometry were compared to single and consensus expression sequence tags in databases and to the E. tenella genome (not annotated). Among the set of unknown proteins analysed, 12 new assignments were proposed on the basis of similarities with Apicomplexa proteins. In order to define sporozoite proteins as potential targets for coccidiosis therapy, proteins were studied according to their relative abundance and immunogenicity in the sporozoite. Immunoblots of sporozoite 2D maps with chicken sera were performed and approximately 50 proteins were defined as antigens. It was shown that abundance and immunogenicity are not related in the sporozoite stage. Perspectives of gene prediction and completion of the genome annotation by a proteomic approach is discussed.

Amino Acid Sequence↗

PubMed2005

Recent studies on the electrospray ionisation mass spectrometric behaviour of selected nitrogen-containing drug molecules and its application to drug analysis using liquid chromatography-electrospray ionisation mass spectrometry.

This review presents recent studies on the electrospray ionisation mass spectrometry (ESI-MS) of selected N-containing drug molecules, their metabolites, formulation degradation products and process impurities taken from both studies in the author's laboratory and the recent literature using the Web of Knowledge database. Molecules of mass less than 500 Da are chosen according to selected structural classes in which they give ESI signals primarily in the positive ion mode as [M+H]+ ions. The structural classes are drugs with amine-containing side chains, drugs with N-containing saturated ring structures, drugs with N-containing unsaturated ring structures and quaternary ammonium drugs. Details are given on the fragmentations, where available, that these ionic species exhibit in-source and in ion-trap, triple quadrupole and time-of flight mass spectrometers. Fragmentation data, again where available, using electron impact mass spectrometry (EI-MS) is included for comparison. A review of applications for the period 2004-2005, again taken from the Web of Knowledge database, of the technique liquid chromatography-electrospray ionisation mass spectrometry (LC-ESI-MS) to the detection and determination of these N-containing drug molecules in biomatrices, pharmaceutical formulations, etc., is then made. Analytical information on, for example, sample concentration techniques, LC separation conditions, recoveries from biological media, degradation products and limits of detection (LODs) are provided. Comparisons, where available, are also made with rival analytical techniques such as gas liquid chromatography-mass spectrometry (GLC-MS), capillary electrophoresis-electrospray ionisation mass spectrometry (CE-ESI-MS) and stripping voltammetry (SV).

Amines↗

PubMed2005

Sustainable pattern analysis of a publicly owned Material Recovery Facility in a fast-growing urban setting under uncertainty.

Sustainable development goals are achievable through the installation of Material Recovery Facilities (MRFs) in certain solid waste management systems, especially those in rapidly expanding multi-district urban areas. MRFs are a cost-effective alternative when curbside recycling does not demonstrate long-term success. Previous capacity planning uses mixed integer programming optimization for the urban center of the city of San Antonio, Texas to establish that a publicly owned material recovery facility is preferable to a privatized facility. As a companion study, this analysis demonstrates that a MRF alleviates economic, political, and social pressures facing solid waste management under uncertainty. It explores the impact of uncertainty in decision alternatives in an urban environmental system. From this unique angle, waste generation, incidence of recyclables in the waste stream, routing distances, recycling participation, and other planning components are taken as intervals to expand upon previous deterministic integer-programming models. The information incorporated into the optimization objectives includes economic impacts for recycling income and cost components in waste management. The constraint set consists of mass balance, capacity limitation, recycling limitation, scale economy, conditionality, and relevant screening restrictions. Due to the fragmented data set, a grey integer programming modeling approach quantifies the consequences of inexact information as it propagates through the final solutions in the optimization process. The grey algorithm screens optimal shipping patterns and an ideal MRF location and capacity. Two case settings compare MRF selection policies where optimal solutions exemplify the value of grey programming in the context of integrated solid waste management.

Algorithms↗

PubMed1999

YAC fragmentation with repetitive and single-copy sequences: detailed physical mapping of the presenilin 1 gene on chromosome 14.

We constructed new LYS2 fragmentation vectors that allow direct acentric and centric fragmentation of yeast artificial chromosomes (YACs) and selection of fragmented YACs in yeast strain AB1380. The fragmentation vectors were used efficiently with repetitive (e.g., Alu), low-copy (e.g., CA-repeats) and single-copy (e.g., exons) sequences. High recombination efficiencies were obtained in fragmenting two different CEPH YACs with the Alu consensus sequence as target sequences for homologous recombination. Analysis of the acentric Alu fragmentation panel of 788H12, containing the presenilin 1 (PSEN1) gene for familial Alzheimer's disease (AD), indicated that high-resolution YAC fragmentation panels covering the entire parent YAC are obtained. Also, marker content analysis of the fragmentation panel indicated that fragmented YACs were propagated stably without rearrangements. The same fragmentation vectors were used efficiently for fragmentation of 788H12 with unique sequences, i.e., exons 3 and 12 of PSEN1 and D14S77, a polymorphic CA repeat, as target sequences. Together, our YAC fragmentation data of 788H12 provided a size estimate for the coding region of PSEN1 of 60kb and a more precise localization of D14S77 at 25kb upstream of PSEN1.

Alu Elements↗

PubMed2002

Separation and identification of phosphatidylserine molecular species using reversed-phase high-performance liquid chromatography with evaporative light scattering and mass spectrometric detection.

A reversed-phase HPLC method compatible with evaporative light scattering (ELS) and electrospray mass spectrometric (ES-MS) detection was developed for separation of phosphatidylserine (PS) molecular species. The method was optimised for separation of three disaturated synthetic species: dipalmitoyl glycerophosphoserine, palmitoyl-stearoyl glycerophosphoserine and distearoyl glycerophosphoserine using isocratic elution with a mixture of 2-propanol, tetrahydrofuran and ammonium formate. Baseline separation was obtained on three different columns: one polystyrene/divinylbenzene (PS/DVB) column and two silica based C(18) and C(30) columns. The best chromatographic resolution was achieved with the C(30) column. The limit of detection for DPPS was 5 microg/ml (S/N=3) with ELS detection and 0.1 microg/ml (S/N=3) with negative ion ES-MS in the single ion monitoring mode. Baseline separation of the five main species in a biological PS sample, bovine brain PS, was obtained with the PS/DVB column. Species identification was done by using the retention times of the intact PS species and their corresponding carboxylate anion fragments obtained by in-source fragmentation. Data have shown that individual PS species can be identified by their retention times using direct ELS detection in a mixture of disaturated PS species. However, for the bovine brain PS electrospray-MS detection was necessary for species identification due to the many possible fatty acid combinations in biological PS.

Animals↗

PubMed2005

LC-MSn methods for saccharide characterization of monoglycosyl flavonoids using postcolumn manganese complexation.

A simple tandem mass spectrometry method for differentiating isomeric monoglycosyl flavonols, flavones, and flavanones using manganese complexation is reported. Dissociation of the [Mn(II) (L) (L - H)]+ and [Mn(II) (L)2 (L - H)]+ species provides unique fragment ions that allow the identification of the saccharide moiety as glucose, galactose, arabinose, or xylose. The glycosylation site of the flavonoid can also be determined by the fragmentation pathways of the Mn complexes. The Mn complexation method was adapted for on-line liquid chromatography-mass spectrometry analysis and tested using flavonoid extracts from Fuji apples (Malus domestica Borkh. cv. Fuji) and red onions (Allium cepa L.). Using fragmentation data obtained from collisional activated dissociation of the deprotonated flavonoid glycosides and their Mn complexes, the major flavonoid species in these extracts were identified.

Chromatography, Liquid↗

PubMed2003

Solvent coordination in gas-phase [Mn.(H(2)O)(n)](2+) and [Mn.(ROH)(n)](2+) complexes: theory and experiment.

An experimental gas-phase study of the intensities and fragmentation patterns of [Mn.(H(2)O)(n)](2+) and [Mn.(ROH)(n)](2+) complexes shows the combinations [Mn.(H(2)O)(4)](2+) and [Mn.(ROH)(4)](2+) to be stable. Evidence in complexes involving the alcohols methanol, ethanol, 1-propanol, and 2-propanol favors preferential fragmentation to [Mn.(ROH)(4)](2+), whereas the fragmentation data for water is less clear. Supporting density functional calculations show that both [Mn.(H(2)O)(4)](2+) and [Mn.(MeOH)(4)](2+) adopt stable tetrahedral configurations, similar to those proposed for biochemical systems where solvent availability and coordination is restricted. Calculated incremental binding energies show a gradual decline on going from one to six solvent molecules, with a step occurring between four and five molecules. The addition of further solvent molecules to the stable [Mn.(MeOH)(4)](2+) unit shows a preference for [Mn.(MeOH)(4)(MeOH)(1,2)](2+) structures, where the extra molecules occupy hydrogen-bonded sites in the form of a secondary solvation shell. Very similar behavior is seen on the part of water. As part of an analysis of the experimental data, the calculations have explored the influence different spins states of Mn(2+) have on solvent geometry. It is concluded that the experimental observations are best reproduced when the central Mn(2+) ion is in the high-spin (6)S ground state. The results are also considered in terms of the biochemical activity of Mn(2+) where the ion is capable of isomorphous substitution with Zn(2+), which itself exhibits a preference for tetrahedral coordination.

Journal Article↗

PubMed2003

High-performance liquid chromatography (HPLC) analysis of phenolic compounds in berries with diode array and electrospray ionization mass spectrometric (MS) detection: ribes species.

High-performance liquid chromatography combined with diode array and electrospray ionization mass spectrometric (MS) detection was used to study phenolic compounds in berries of black, green, red, and white currants (Ribes spp.). UV-visible spectrometry was a valuable tool for the identification of the class of the phenolic compound, whereas MS and MS-MS fragmentation data were useful for further structural characterization. Distinct similarities were found in the relative distribution of conjugated forms of phenolic compounds among the four currants. Phenolic acids were found mainly as hexose esters. Flavonol glycosides and anthocyanin pigments were mainly found as 3-O-rutinosides and second as 3-O-glucosides. However, cyanidin 3-O-sambubioside and quercetin hexoside-malonate were notable phenolic compounds in red currant. Flavonol hexoside-malonates were identified and quantified in the berries of currants for the first time.

Anthocyanins↗

PubMed2005

Determination of the phytoalexin resveratrol (3,5,4'-trihydroxystilbene) in peanuts and pistachios by high-performance liquid chromatographic diode array (HPLC-DAD) and gas chromatography-mass spectrometry (GC-MS).

The phytoalexin resveratrol (3,5,4'-trihydroxystilbene) in edible peanut (Arachis hypogaea L.) and pistachio (Pistacia vera L.) varieties grown in Turkey was analyzed by high-performance liquid chromatographic diode array and gas chromatography-mass spectrometric detection. trans-Resveratrol in six peanut varieties, five pistachio varieties, and four market samples ranged between 0.03 and 1.92 microg/g. The Cerezlik 5025 peanut (1.92 +/- 0.01 microg/g) and Ohadi pistachio genotype (1.67 +/- 0.01 microg/g) had significantly higher trans-resveratrol contents. Peanuts contained 0.03-1.92 microg/g (av = 0.84 microg/g) of trans-resveratrol, whereas pistachio contained 0.09-1.67 microg/g (av = 1.15 microg/g). With exposure to UV light for 1 min, trans-resveratrol concentrations of samples ranged from 0.02 to 1.47 microg/g and those of cis-resveratrol from 0.008 to 0.32 microg/g. The occurrence of resveratrol in peanut and pistachio was confirmed by total ion chromatograms (TIC) of bis[trimethylsilyl]trifluoroacetamide derivatives of resveratrol isomers and comparison of the mass spectral fragmentation data with those of a resveratrol standard. Formation of the cis-isomer in pistachios was higher than in peanuts.

Arachis↗