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PubMed2006

Selective detection and identification of phosphorylated proteins by simultaneous ligand-exchange fluorescence detection and mass spectrometry.

A ligand-exchange method for the detection and identification of phosphorylated peptides in complex mixtures is presented that is based on the characterization of phosphorylated species by solution-phase interactions with Fe(III) ions and subsequent fluorescence readout. After the separation of the peptides and digest products on a reversed-phase LC column, the flow is split between the two detection systems. One part is directed towards an electrospray mass spectrometer for direct detection and identification of all the peptides present in the sample. The other part of the flow is directed towards a ligand-exchange detection system. This system relies on the specific release of a fluorescent reporter ligand from a Fe(III)-complex in the presence of phosphorylated peptides. To recognize false positive signals due to high-affinity non-phosphorylated high-acidic peptides and other compounds which are known to be a problem in for instance immobilized metal affinity chromatography (IMAC), a second run is performed after incubation of the sample with alkaline phosphatase. A positive signal in this second run indicates a high-affinity non-phosphorylated compound. The method is illustrated using digest from a phosphorylated alpha-casein. Automated switching between MS and MS-MS was performed to obtain additional information about the compounds present in the sample. The linearity of the method was tested in the range of 0.5-80 microM of phosphorylated peptides. A limit of detection (LOD) of 0.5 microM was obtained for a mono-phosphorylated peptide. The interday (n=4) and intraday precision (n=3) expressed as relative standard deviation was better than 10%.

Caseins↗
PubMed1992

Identification of immunodominant antigens during infection with Mycobacterium tuberculosis.

T lymphocytes isolated from mice infected with Mycobacterium tuberculosis response vigorously to proteins secreted by the bacilli and these antigens may be of importance in the generation of protective immunity against the disease. In this study, short-term culture filtrate (ST-CF), which constitutes a complex mixture of secreted proteins, was fractionated by a modified preparative SDS-PAGE technique. The ability of each fraction to be recognized by T cells isolated from infected mice was evaluated by quantifying proliferation and IFN-gamma production in cell cultures. Two molecular mass regions 4-11 and 26-35 kDa were found to possess marked stimulatory properties. Four potent single antigens were mapped within the stimulatory regions. These purified antigens stimulated T cells isolated from mice at the height of a tuberculous infection to produce large amounts of IFN-gamma. Two of these stimulatory antigens belonged to the antigen 85 complex.

Analysis of Variance↗
PubMed1991

Molecular characterization of human immunodeficiency virus type 1 cloned directly from uncultured human brain tissue: identification of replication-competent and -defective viral genomes.

All presently available replication-competent proviral clones of human immunodeficiency virus type 1 (HIV-1) are derived from cell culture-amplified virus. Since tissue culture is highly selective for viral strains with an in vitro growth advantage, such clones may not be representative of the biologically relevant virus present in vivo. In this study, we report the molecular cloning and genotypic characterization of 10 HIV-1 genomes directly from uncultured brain tissue of a patient with AIDS dementia complex. Targeting unintegrated circular HIV-1 molecules for recombinant lambda phage cloning, we obtained four full-length genomes with one or two long terminal repeats (LTRs), three defective genomes with internal deletions, two rearranged genomes with inverted LTR sequences, and one integrated proviral half with flanking cellular sequences. Nucleotide sequence analysis of these clones demonstrated chromosomal integration, circle formation, genomic inversion, and LTR-mediated autointegration of HIV-1 genomes in vivo. Comparison of a 510-bp hypervariable envelope region among 8 lambda phage-derived and 12 polymerase chain reaction-derived clones from the same brain specimen identified a predominant viral form as well as genetically divergent variants. Variability among 19 of 20 clones ranged between 0.2 and 1.2%. One clone exhibited 8.2% nucleotide sequence differences consisting almost exclusively of G-to-A changes. Transfection of the four full-length HIV-1 genomes identified one clone (YU-2) as replication competent and exhibiting growth characteristics similar to those of tissue culture-derived macrophage tropic strains of HIV-1. These results demonstrate, for the first time, that replication-competent HIV-1 genomes, complex mixtures of defective viral forms, and chromosomally integrated provirus persist in vivo. In addition, the brain-derived viral clones are expected to prove valuable for future studies of macrophage and neurotropism as well as for the analysis of other viral properties that are subject to in vitro selection pressures.

AIDS Dementia Complex↗
PubMed2003

Simple detection method of powerful antiradical compounds in the raw extract of plants and its application for the identification of antiradical plant constituents.

A simple detection method for a powerful radical scavenging compound in a mixture containing a large variety of compounds, such as the raw extract of edible plants, was developed using 1,1-diphenyl-2-picrylhydrazyl (DPPH) as the radical reagent. The method was established on the basis of the features of the typical chain-breaking antioxidation reaction mechanism, which suggests that the radical scavenging antioxidant should be converted to other stable nonradical compounds during the reaction. This method requires only a simple HPLC instrument, and the disappearance or decrease in the peak intensity, which is induced by the addition of DPPH. This change is monitored by the HPLC to detect the powerful radical scavenger from the complex mixture. The method was applied to the detection and identification of the most powerful antiradical compound in the extracts of three antioxidatively active plant extracts (Psidium guajava, Citrus depressa, and Hypericum chinense). The radical scavenging efficiency of a newly identified compound from H. chinense was also compared with that of Trolox and catechin using the method.

Antioxidants↗
PubMedDate not supplied

Modern strategies for protein quantification in proteome analysis: advantages and limitations.

Over the last 3 years, a number of mass spectrometry-based methods for the simultaneous identification and quantification of individual proteins within complex mixtures have been reported. Most, if not all, of such strategies apply a two-step approach: the first for the separation of proteins or peptides, and the second uses mass spectrometry to identify and quantify the individual components. To simplify the outcome of both steps, certain chemicals and heavy-isotope-labeling are commonly used in the early stages of sample preparation (except in differential fluorescence labeling protocols). The ultimate goal of these strategies is to be able to identify every protein expressed in a cell or tissue, and to determine each protein's abundance, state of modification, and possible involvement in multi-protein complexes. In this review, an attempt is made to highlight the salient characteristics of the existing strategies with particular attention to their strengths and weaknesses.

Animals↗
PubMedDate not supplied

GLC and GLC-mS analysis of thiophene derivatives in plants and in in vitro cultures of Tagetes patula L. (Asteraceae).

The occurrence of thiophenic compounds in diverse plant organs and in in vitro root-, callus- and cell suspension cultures of Tagetes patula cv. Carmen was investigated using capillary GLC and GLC-MS. The separation of thiophenes by capillary GLC and the group specific MS fragmentation with the typical sulfur isotope peaks allowed the unequivocal assignment of individual thiophenes in complex mixtures, even when occurring in traces and in the presence of different geometrical isomers. The extracts of Tagetes patula cv. Carmen contained the following 8 thiophene compounds: 5-(3-buten-1-ynyl)-2,2'-bithienyl (BBT), 5'-methyl-5-(3-buten-1-ynyl)-2,2'-bithienyl (MeBBT), 5-(1-pentynyl)-2,2'-bithienyl (PBT), 5-(4-hydroxy-1-butynyl)-2,2'-bithienyl (BBTOH), 2,2',5,2"-terthienyl (alpha-T), 5-(4-acetoxy-1-butynyl)-2,2'-bithienyl (BBTOAc), 5-methylaceto-5'-(3-buten-1-ynyl)-2,2'-bithienyl (AcOCH2BBT), and 5-(3,4-diacetoxy-1-butynyl)-2,2'-bithienyl (BBT(OAc)2). The most complex thiophene profile, including the less common PBT was detected in aerial parts of freshly harvested plant material. Under in vitro conditions only the root cultures, but not callus or cell suspension cultures produced substantial amounts of irregular thiophenes confirming that roots are the main site of thiophene biosynthesis.

Asteraceae↗
PubMed2004

Capillary electrophoresis-mass spectrometry for glycoscreening in biomedical research.

Application of capillary electrophoresis (CE) in combination with mass spectrometry (MS) and tandem MS to glycoscreening in biomedical projects is highlighted. In the first part recent CE-MS experiments by sheath liquid CE and multiple stage MS are reported. Neutral and negatively charged N-glycan mixtures from ribonuclease B and fetuin, high-mannose type N-glycoforms, oligosaccharides from lipopolysaccharides (LPS) of Haemophilus influenzae, polysaccharides of Pseudomonas aeruginosa and Staphylococcus aureus were analyzed. A particular emphasis is devoted to the applicability of novel off- and on-line CE-MS and tandem MS methods for screening of proteoglycan-derived oligosaccharides, glycosaminoglycans (GAGs), such as hyaluronates from Streptococcus agalactiae, chondroitin/dermatan sulfates (CS/DS) from bovine aorta and human skin fibroblast decorin, and heparin/heparan sulfate (HS) from porcine and bovine mucosa. The performance of CE-MS/MS for identification of glycoforms in glycopeptides and glycoproteins is illustrated by experiments performed on complex mixtures from urine of patients suffering from a hereditary N-acetylhexosaminidase deficiency (Schindler's disease) and urine of patients suffering from cancer cachexia. For determination of glycosylation patterns in glycoproteins like enzymes and antibodies by CE/MS, both CE-matrix assisted laser desorption/ionization (MALDI) and CE-electrospray ionization (ESI)-MS were functional. Finally, the potential of CE-ESI-MS strategy in glycolipid analysis is demonstrated for gangliosides from bovine brain for which particular CE buffer conditions are required.

Animals↗
PubMed1985

Preparative elution of proteins from nitrocellulose membranes after separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

Various conditions were analyzed and optimized for the preparative elution of proteins from nitrocellulose membranes after transfer from sodium dodecyl sulfate (SDS)-polyacrylamide gels. The efficiency of elution was best using pyridine or acetonitrile elution solvents, intermediate for buffer containing a mixture of sodium dodecyl sulfate, Triton X-100, and sodium deoxycholate, and negligible for buffers containing any single detergent or chaotropic salt, such as urea or guanidine hydrochloride. The efficiency of elution with any solvent also depended on the molecular weight of the proteins, smaller proteins being more easily removed from membranes. As a general procedure, proteins may be eluted from nitrocellulose membranes by incubation with either 40% acetonitrile or 50% pyridine in 0.1 M ammonium acetate, pH 8.9, for 1-3 h at 5-37 degrees C. The recommended procedures for protein elution appear to offer a rapid, simple, and efficient means of recovering proteins from complex mixtures after separation by SDS-PAGE and transfer to nitrocellulose membranes.

Acetonitriles↗
PubMed1991

Mass profile monitoring in trace analysis by gas chromatography/mass spectrometry.

The advantages of gas chromatography/mass spectrometry (GC/MS) selected-ion monitoring (SIM) in the mass profile (MP) mode at medium mass resolving power were investigated for analyses requiring detection of low-picogram quantities of analytes in complex mixtures. The mass profile monitoring provides a certainty at least 10 times greater than that achieved by conventional GC/MS-SIM in the peak-top monitoring mode, and it can be operated at lower mass resolving power to compensate for the loss of sensitivity in the MP mode. The examination of mass profile peak shape, central mass shift, and sequential changes during GC elution not only reveals the presence of interfering compounds but also results in accurate mass measurement for those interferences. The latter feature takes the MP mode beyond the target mass analysis that GC/MS-SIM was originally designed for. This additional dimension of information is particularly useful for those complex and incompletely characterized matrices that are frequently encountered in environmental and biological sample analyses.

Animals↗
PubMed2007

Screening of acetylcholinesterase inhibitors in natural extracts by CE with electrophoretically mediated microanalysis technique.

An electrophoretically mediated microanalysis (EMMA) method for screening acetylcholinesterase (AChE) inhibitors in natural extracts is described. In this method, solutions of AChE and the mixture of the substrate and the natural extract were successively injected into the capillary, and mixed electrophoretically by applying a voltage for a short time. Afterwards the voltage was reapplied to separate the product from the unreacted substrate and the natural extract. The measured peak area of the product at UV 230 nm represents the enzyme activity. Since the extract is mixed with the substrate, there is no need to separate the components before testing the inhibition. The inhibitory activity of the natural extract as a whole can be easily found if the peak area of the product is reduced. This makes the present method suitable for screening inhibitors in complex mixtures, such as natural extracts. Compared to the commonly used spectrometric method for screening of AChE inhibitors, the major advantage of the present method is the elimination of Ellman reagent, which is essential for the spectrometric method. This not only simplifies the experimental procedure but also minimizes false-positive results. Moreover, it is an obvious advantage of combining the separation power with the on-column enzyme assay for further investigating which compound(s) is/are responsible for the inhibition. The method was validated using a commercially available AChE inhibitor tacrine and a small chemical library containing four AChE inhibitors and 32 natural extracts. Inhibitors in natural extracts were identified with the present method.

Acetylcholinesterase↗
PubMed2004

Subviral DNAs associated with geminivirus disease complexes.

Ageratum conyzoides (ageratum) is a common and widespread weed species that may act as a reservoir host for geminivirus diseases. Ageratum plants growing in Singapore and exhibiting yellow vein disease are infected with a complex mixture of viral, subviral and recombinant DNA components. This whitefly-transmitted disease is caused by the monopartite begomovirus ageratum yellow vein virus (AYVV) in association with a recently discovered satellite component referred to as DNA beta. Diseased plants also contain a subviral component, referred to as DNA 1, that has probably become associated with the begomovirus and adapted to whitefly transmission during mixed infection with an aphid-transmitted nanovirus. Unlike DNA beta, the nanovirus-like component is not essential for the disease. Recombination between the viral and subviral DNAs occurs frequently and may play an important evolutionary role by generating component diversity. The identification of a similar complex associated with cotton leaf curl disease (CLCuD), a serious constraint to cotton growing in Pakistan, and the isolation of DNA beta homologues from diverse plant species growing in widespread geographical locations suggests that such disease complexes are common and may have a significant impact on agriculture in the eastern hemisphere.

Ageratum↗
PubMed2001

A reproducible approach to the reporting of organochlorine compounds in epidemiologic studies.

A growing body of research indicates that the most biologically active PCB congeners and organochlorines are not the most abundant components in human and wildlife samples. As researchers attempt measurement on a wider pool of less abundant compounds, they inevitably face quantification problems. To address this problem and enhance comparability across studies, we propose a standardized approach to report organochlorines that is based on a reproducible method to determine the limit of quantification (LQ). Two statistical methods are incorporated into our approach, one by Gibbons termed the Alternative Minimum Level (AML), and one based on determining a region of stable relativestandard deviation in instrument response (RSD). We illustrate our approach using historical samples collected during the 1960s from a cohort of pregnant women enrolled in the Child Health and Development Study. The results are applicable to determining the LQ of any method, and are of utmost importance to environmental scientists conducting trace organic analyses of complex mixtures. Our results demonstrate that: (1) precision as measured by RSD is the most important criterion in determining LQ; (2) the AML routinely isolates a region of constant RSD; and (3) the precision of the instrument detector response as measured with pure standards locates the LQ applicable for real samples - that is, the true limits of quantification reside in the detector, not the matrix effects or analyte recoveries associated with real samples. A corollary of these findings is that bias due to matrix effects and analyte recoveries can be assessed separately from precision and LQdetermination. Previous approaches involved spiking matrix blanks to determine LQ, a problematic strategy for real world, complex matrices. We have now validated the use of pure standards in LQ determination, an approach that is practical and accessible to most analysts.

Animals↗
PubMed1998

Rapid molecular mass and structural determination of plant cell wall-derived oligosaccharides using off-line high-performance anion-exchange chromatography/mass spectrometry.

A method has been developed for the rapid molecular mass determination and structural elucidation of mixtures of oligosaccharides derived from plant cell walls. The oligosaccharides were fractionated using gel permeation chromatography and 'analytical' high-performance anion-exchange chromatography (HPAEC), neutralized, dried and the mixtures of eluent salt and oligosaccharides were per-O-acetylated directly. The derivatized oligosaccharides were isolated by dissolution in dichloromethane and the salts were removed by aqueous partitioning. The per-O-acetylated oligosaccharides were analysed using electrospray (ES) and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MS). Exploiting the fact that acid-catalysed per-O-acetylation of oligosaccharides can be achieved even under the extremely salty conditions that are found in post-column neutralized HPAEC fractions, and combining this derivatization step with off-line ESMS, allow rapid screening for molecular mass and thus yield information on the composition of the various oligosaccharides in these complex mixtures. Subsequent per-O-methylation of the per-O-acetylated, salt-free fractions and collision-induced dissociation tandem mass spectrometric analysis was used for additional sequence and branching determination of the oligosaccharides.

Carbohydrate Sequence↗
PubMed1997

Drinking water and cancer.

Epidemiologic evidence on the relation between contaminants in drinking water and cancer is reviewed. The reviewed studies cover exposure to: disinfection byproducts; nitrate; arsenic and other metals; volatiles and contaminants from hazardous waste sites; asbestiform fibers; radionuclides; and fluoride. Most investigations are ecologic, with some confirmation of elevated risk from individual-based studies. In the case of waterborne arsenic, and possibly chlorination byproducts, there is a consistent but small body of epidemiologic evidence of an association with one or more types of cancer. Nitrate in groundwater has increased greatly over the years, and the demonstration of endogenous nitrosation among highly exposed subjects raises concern of elevated cancer risk. However, the epidemiologic data are not yet sufficient to draw a conclusion. There is a diversity of studies among populations exposed to water contaminated with pesticides, volatile organics, or mixtures from hazardous waste sites. Studies of asbestiform fibers and radionuclides in water are not conclusive, but there are suggested elevations of several cancer sites in highly exposed populations. There is no suggestion that fluoride in drinking water is linked with elevated risk of cancer. As topics for epidemiologic evaluation, drinking water contaminants pose methodologic problems common to studies designed to detect relatively small elevations in risk, with the added challenge of assessing exposures for many years in the past. Nevertheless, epidemiologic assessment is valuable and clearly warranted, given the potential public health impact of small risk elevations among very large exposed populations, and the limitations of toxicologic experiments in assessing carcinogenic risk of complex mixtures or of compounds for which appropriate animal models are not available.

Animals↗
PubMed2005

Estrogen-active nonylphenols from an isomer-specific viewpoint: a systematic numbering system and future trends.

4-Nonylphenols (NPs) are very important environmentally relevant substances. They are persistent, toxic, endocrine-disrupting chemicals that are priority hazardous substances of the EU Water Framework Directive. NPs are degradation products of 4-nonylphenol ethoxylates (NPEs), a widely used group of nonionic surfactants. The technical synthesis of NP leads to a complex mixture of NPs consisting of isomeric compounds that have different branched nonyl side chains. It has recently become clear that an isomer-specific view is absolutely necessary when it comes to correctly evaluating the biological effects of NPs and their behavior in the environment, including degradation processes. To rationalize the identification of individual NP isomers in scientific studies, we have developed a numbering system for all possible NP isomers that follows the IUPAC rules of substituent characterization in alkylphenols. The 211 possible constitutional isomers of NP are numbered according to a hierarchical and logical system. In the future, multidimensional coupling systems--for example GCxGC-TOF-MS--will be needed to study these highly complex class of substances.

Chemistry, Organic↗
PubMed2001

Separation and identification of phospholipid peroxidation products.

The molecular species in mixtures of phospholipid hydroperoxides are difficult to separate and identify by typical chromatographic and mass spectrometric techniques. As reported by Havrilla and coworkers, silver ion coordination ion-spray mass spectrometry (CIS-MS) has proven to be a powerful technique for the identification of mixtures of hydroperoxides. This ionization technique, which involves the formation of Ag+ adducts of the hydroperoxides, provides valuable, unambiguous structural information about the hydroperoxides. Herein, we report a method for the analysis and identification of phospholipid hydroperoxides using CIS-MS. We also report an improved method for the separation of phospholipid hydroperoxides by reversed-phase high-performance liquid chromatography (RP-HPLC), which, for the first time, separates some of the hydroperoxide isomers. CIS-MS can be coupled with this RP-HPLC method by the addition of AgBF4 to the mobile phase or to the HPLC effluent postcolumn, thus allowing powerful HPLC-MS techniques to be used to identify complex mixtures of phospholipid hydroperoxides.

Arachidonic Acid↗
PubMed2001

Whole genome sequencing of meticillin-resistant Staphylococcus aureus.

BACKGROUND: Staphylococcus aureus is one of the major causes of community-acquired and hospital-acquired infections. It produces numerous toxins including superantigens that cause unique disease entities such as toxic-shock syndrome and staphylococcal scarlet fever, and has acquired resistance to practically all antibiotics. Whole genome analysis is a necessary step towards future development of countermeasures against this organism. METHODS: Whole genome sequences of two related S aureus strains (N315 and Mu50) were determined by shot-gun random sequencing. N315 is a meticillin-resistant S aureus (MRSA) strain isolated in 1982, and Mu50 is an MRSA strain with vancomycin resistance isolated in 1997. The open reading frames were identified by use of GAMBLER and GLIMMER programs, and annotation of each was done with a BLAST homology search, motif analysis, and protein localisation prediction. FINDINGS: The Staphylococcus genome was composed of a complex mixture of genes, many of which seem to have been acquired by lateral gene transfer. Most of the antibiotic resistance genes were carried either by plasmids or by mobile genetic elements including a unique resistance island. Three classes of new pathogenicity islands were identified in the genome: a toxic-shock-syndrome toxin island family, exotoxin islands, and enterotoxin islands. In the latter two pathogenicity islands, clusters of exotoxin and enterotoxin genes were found closely linked with other gene clusters encoding putative pathogenic factors. The analysis also identified 70 candidates for new virulence factors. INTERPRETATION: The remarkable ability of S aureus to acquire useful genes from various organisms was revealed through the observation of genome complexity and evidence of lateral gene transfer. Repeated duplication of genes encoding superantigens explains why S aureus is capable of infecting humans of diverse genetic backgrounds, eliciting severe immune reactions. Investigation of many newly identified gene products, including the 70 putative virulence factors, will greatly improve our understanding of the biology of staphylococci and the processes of infectious diseases caused by S aureus.

Animals↗