Genome-wide pharmacogenetic investigation of a hepatic adverse event without clinical signs of immunopathology suggests an underlying immune pathogenesis.

One of the major goals of pharmacogenetics is to elucidate mechanisms and identify patients at increased risk of adverse events (AEs). To date, however, there have been only a few successful examples of this type of approach. In this paper, we describe a retrospective case-control pharmacogenetic study of an AE of unknown mechanism, characterized by elevated levels of serum alanine aminotransferase (ALAT) during long-term treatment with the oral direct thrombin inhibitor ximelagatran. The study was based on 74 cases and 130 treated controls and included both a genome-wide tag single nucleotide polymorphism and large-scale candidate gene analysis. A strong genetic association between elevated ALAT and the MHC alleles DRB1(*)07 and DQA1(*)02 was discovered and replicated, suggesting a possible immune pathogenesis. Consistent with this hypothesis, immunological studies suggest that ximelagatran may have the ability to act as a contact sensitizer, and hence be able to stimulate an adaptive immune response.

Electrospray ionization tandem mass spectrometric study of salt cluster ions: part 2--salts of polyatomic acid groups and of multivalent metals.

Salt cluster ions formed from 0.05 M solutions of CaCl(2), CuCl(2) and Na(A)B (where A = 1 or 2 and B = CO(3)(2-), HCO(3)(-), H(2)PO(4)(-) and HPO(4)(2-)) were studied by electrospray ionization tandem mass spectrometry. The effects on salt cluster ions of droplet pH and of redox reactions induced by electrospray provide information on the electrospray process. CaCl(2) solution yielded salt cluster ions of the form (CaCl(2))(n)(CaCl)(x)(x+) and (CaCl(2))(n)(Cl)(y)(y-), where x, y = 1-3, in positive- and negative-ion modes, respectively. Upon collision induced dissociation (CID), singly charged CaCl(2) cluster ions fragmented, doubly charged cluster ions generated either singly or both singly and doubly charged fragment ions, depending on the cluster mass, and triply charged clusters fragmented predominantly by the loss of charged species. CuCl(2) solution yielded nine series of cluster ions of the form (CuCl(2))(n)(CuCl)(m) plus Cu(+), CuCl(+), or Cl(-). CuCl, the reductive product of CuCl(2), was observed as a neutral component of positively and negatively charged cluster ions. Free electrons were formed in a visible discharge that bridged the gap between the electrospray capillary and the sampling cone brought about the reduction of Cu(2+) to Cu(+). Upon CID, these cluster ions fragmented to lose CuCl(2), CuCl, Cl, and Cl(2). Na(2)CO(3) and NaHCO(3) solutions yielded cluster ions of the form (Na(2)CO(3))(n) plus Na(+) or NaCO(3)(-). Small numbers of NaHCO(3) molecules were found in some cluster ions obtained with the NaHCO(3) solution. For both Na(2)HPO(4) and NaH(2)PO(4) solutions, ions of the form (Na(2)HPO(4))(h), (NaH(2)PO(4))(i), (Na(3)PO(4))(j), (NaPO(3))(k) plus Na(+), PO(3)(-) or H(2)PO(4)(-) were observed. In addition, ions having one or two phosphoric acid (H(3)PO(4)) molecules were observed from the NaH(2)PO(4) solution while ions containing one sodium hydroxide (NaOH) molecule were observed from the Na(2)HPO(4) solution. The cluster ions observed from these four salts of polyatomic acid groups indicate that changes in pH occur in both directions during the electrospray process principally by solvent evaporation; the pH value of the acidic solution became lower and that of the basic solution higher.

Estrogenic potency of chemicals detected in sewage treatment plant effluents as determined by in vivo assays with Japanese medaka (Oryzias latipes).

Gonadal intersex and high prevalences of the female phenotype have been observed in fish populations in urbanized areas. Environmental estrogens discharged in sewage treatment plant effluents may be responsible for feminization of fish but many compounds with the potential to induce these responses occur in effluents, including natural and synthetic estrogen hormones, degradation products of alkylphenol ethoxylate surfactants, and plasticizers. In this study, the estrogen hormones 17 alpha-ethinylestradiol, 17 beta-estradiol, estrone, and estriol induced intersex (i.e., testis-ova) and altered sex in Japanese medaka (Oryzias latipes) when these fish were exposed to nanogram per liter concentrations of test compounds from hatch to approximately 100 d after hatch. A mix of nonylphenol mono- and diethoxylate induced a weak response and a mix of nonylphenol mono- and diethoxycarboxylate did not give a response in this assay at microgram per liter concentrations, indicating that these degradation products of nonylphenol ethoxylates have little or no estrogenic activity in fish. Bisphenol A induced testis-ova in medaka exposed to a concentration of 10 micrograms/L, but diethylhexyl phthalate did not induce a response. Results with the medaka assay were consistent with estrogenic responses in the yeast estrogen screening assay. Analyses of monitoring data reported in the literature indicate that concentrations of estrogen hormones detected in the final effluents of sewage treatment plants are generally greater than the lowest-observed-effect levels for alterations to gonadal development in medaka.

Electrospray ionization tandem mass spectrometric study of salt cluster ions. Part 1--investigations of alkali metal chloride and sodium salt cluster ions.

Salt cluster ions of alkali metal chlorides ACl (A = Li(+), Na(+), K(+), Rb(+) and Cs(+)) and sodium salts NaB (B = I(-), HCOO(-), CH(3)COO(-), NO(2)(-), and NO(3)(-)), formed by electrospray ionization, were studied systematically by mass spectrometry. The influences on the total positive ion and negative ion currents of variation of solvent, solution concentration, desolvation temperature, solution flow-rate, capillary voltage and cone voltage were investigated. Only cone voltage was found to influence dramatically the distribution of salt cluster ions in the mass spectra observed. Under conditions of normal cone voltage of approximately 70 V, cluster ions having magic numbers of molecules are detected with high relative signal intensity. Under conditions of low cone voltage of approximately 10 V, the distribution of cluster ions detected is characterized by a relatively low average mass/charge ratio due to the presence of multiply charged cluster ions; in addition, there is a marked reduction in cluster ions having a magic number of molecules. Product ion mass spectra obtained by tandem mass spectrometry of cluster ions are characterized by a base peak having a magic number of molecules that is less than and closest to the number of molecules in the precursor ion. Structures have been proposed for some dications and some quadruply charged ions. At pH 3 and 11, the mass spectra of NaCl clusters show the presence of mixed clusters of NaCl with HCl and NaOH, respectively. The effects of ionic radius on 20 distributions of cluster ions for 10 salts were investigated; however, the fine structure of these effects is not readily discerned.

Observation of Na(+)-bound oligomers of quercetin in the gas phase.

While developing a liquid chromatography/tandem mass spectrometry method for the analysis of the flavonoid quercitin, it was observed that quercetin (3,3',4',5,7-pentahydroxyflavone) exhibited clustering in both the positive and negative ion mode. Two series of positive ion clusters were observed; the first series corresponds to singly charged [2M + Na](+) at m/z 627.2 to [13M + Na](+) at m/z 3947.5, while the second series corresponds to doubly charged [7M + 2Na](2+) at m/z 1080.4 to [25M + 2Na](2+) at m/z 3798.5. In the negative ion mode, the behavior of quercetin parallels that of apigenin (4',5,7-trihydroxyflavone) in that [M + NO(3)](-), [2M + NO(3)](-), and [3M + NO(3)](-) were observed at m/z 364.1, 666.0, and 968.9, respectively; in addition, quercitin clusters with chloride ions ([2M + Cl](-) at m/z 638.9 and [3M + Cl](-) at m/z 940. 9) were observed. The results of tandem mass spectrometric examination of several cluster ions are reported.

Determination of dioxins/furans and PCBs by quadrupole ion-trap gas chromatography-mass spectrometry.

The versatility and sensitivity of the quadrupole ion trap tandem mass spectrometer has been applied to the determination of polychlorodibenzo-p-dioxins (PCDDs) and polychlorodibenzofurans (PCDFs), and of polychlorinated biphenyls (PCBs). A brief introduction to the theory of ion confinement in a quadrupole ion trap permits discussion of ion trajectory stability, mass-selective ion ejection, the frequencies of ion motion, and the role of resonant excitation of ion motion. The tandem mass spectrometric examination of PCDDs and PCDFs eluting and co-eluting from a gas chromatographic column is described. Illustrative examples are given of the analysis of field samples containing PCDDs and PCDFs. A comparison is presented of the performance of each of a quadrupole ion trap tandem mass spectrometer, a triple stage quadrupole mass spectrometer, and a sector instrument of relatively high mass resolution for the determination of PCDDs and PCDFs. This comparison is made with respect to instrument tuning, calibration plots, detection limits, ion signals at low concentration, relative response factors, ionization cross-sections, and the examination of field samples. The application of quadrupole ion trap tandem mass spectrometry to the examination of PCBs is focused upon those PCB congeners that have the greatest toxicity. 39 congeners of the total of 209 PCB congeners have been identified as having the greatest toxicities. Chemical ionization has been used for the determination of co-eluting congeners #77 and #110 where the toxicity of the former is much greater than that of the latter. An analytical protocol, based on the variation of molecular ion fragmentation according to the degree (or absence) of chlorine ortho-substitution, has been proposed for distinguishing between toxic and nontoxic PCB congeners.

A novel variant of the MHC-linked hsp70, hsp70-hom, is associated with rheumatoid arthritis.

The three major histocompatibility complex (MHC)-linked hsp70s have been screened for variation in their 28 kDa C-terminal regions by direct nucleotide sequencing of the corresponding DNA fragments. No amino acid variation was detected in the major heat-inducible hsp70 (encoded by hsp70-1 and hsp70-2), although previously unreported silent mutations were identified in all three of the MHC-linked hsp70 genes. A novel coding polymorphism, a G to A transition, was identified at nucleotide 2763 of hsp70-hom (hom-2763). This dimorphism results in a glutamic acid to lysine alteration at position 602 in the C-terminal domain of hsp70-hom. The frequencies of the A-2763 and G-2763 alleles were calculated to be 27% and 73%, respectively. The hom-2763 dimorphism was characterised in 81 HLA-homozygous cell lines using an ARMS-PCR assay and A-2763 was found to be in strong linkage disequilibrium with DRB1*04 (Pc=1.31 x 10(-7), following Bonferoni's correction). Analysis of 60 rheumatoid arthritis (RA) families, each with an affected sib-pair, revealed an association between hsp70-hom A-2763 and RA using both the transmission disequilibrium test (TDT) and the transmission to sib-pair (Tsp) test (P=0.0038 and P=0.013, respectively). This association may be due to linkage disequilibrium with HLA-DR alleles, but could represent an additional risk factor for RA in the MHC class III region.

Mass spectrometric study of persistent acid metabolites of nonylphenol ethoxylate surfactants.

A mass spectrometric study was carried out on two nonylphenoxycarboxylic acids, NP1EC and NP2EC (where 1 and 2 indicate the number of ethoxylate units attached to the nonylphenoxy moiety), that are persistent metabolites of widely used nonionic surfactant nonylphenol ethoxylates. In a gas chromatographic/mass spectrometric (GC/MS) study of the methyl esters of NP1EC and NP2EC, two series of fragment ions were observed in electron ionization (EI) mass spectra; m/z (179 + 14n, n = 0-7) and m/z (105 + 14n, n = 0-4) for NP1ECMe and m/z (223 + 14n, n = 0-7) and m/z (107 + 14n, n = 0-5) for NP2ECMe. Similarity indices were used to compare quantitatively the mass spectra of isomers. The mass spectra of two isomers were found to be similar whereas those of the remaining isomers were readily distinguishable from each other. The abundant fragment ions of the two NPECMes were investigated further by GC/MS/MS; product ions resulting from cleavage in the alkyl moiety, cleavage in the ECMe moiety and cleavage in both moieties were detected. Possible structures of the nonyl groups in the two esters were inferred. GC/chemical ionization (CI) mass spectra of the NPECMes with isobutane as reagent gas showed characteristic hydride ion-abstracted fragment ions shifted by 1 Da from those in the corresponding EI mass spectra. The sensitivity of a selected ion monitoring quantitation method for the NPECMes is enhanced under CI conditions compared with that under EI conditions. With electrospray ionization MS/MS, [M - H](-) ions of NP1EC (m/z 277) and NP2EC (m/z 321) were observed and, upon collision-induced dissociation of [M - H](-) of each of the two acids, fragment ions of m/z 219 corresponding to deprotonated nonylphenol, were observed in each case. Based on this observation, a rapid, simple and reliable selected product ion quantitation method is proposed for NP1EC and NP2EC.

Mass spectrometry applied to the analysis of estrogens in the environment.

Environmental analytical chemistry has recently changed focus from analysis of non-polar, persistent contaminants (e.g. polychlorinated biphenyls and dioxins) to more polar and labile compounds that interfere with biological processes. For example, natural and synthetic estrogens and their metabolites have been detected in sewage treatment plant effluents at nanogram/liter concentrations that are similar to those at which both total sex reversal and intersex (containing both testes and ova) is induced in fish exposed to these compounds in laboratory experiments. The development of techniques for the analysis of natural and synthetic estrogens in biological fluids (i.e. serum and urine) has been a priority in the biomedical field. However, the recent recognition that estrogen hormones are contaminants in the environment that may contribute to endocrine disruption has focused attention on the need for highly sensitive and specific techniques that are applicable for trace analysis in complex environmental matrices. Three optimized mass spectrometric protocols have been developed for the determination and quantitation of steroid hormones in environmental matrices using gas chromatography/tandem mass spectrometry (GC/MS/MS), liquid chromatography/mass spectrometry selected ion monitoring, (LC/MS - SIM) and liquid chromatography/tandem mass spectrometry (LC/MS/MS). The advantages and disadvantages of each method are presented.

Coupling of a Rydberg electron capture ion source with a quadrupole mass filter.

The coupling of a Rydberg electron capture ion source with a Nermag R10-10H quadrupole mass filter is described. Details are given of the addition to this instrument of a creation cell for atoms excited in Rydberg states. Within the Nermag ion source, such atoms allow attachment of electrons of well-defined thermal energy. SF(6) was used for optimization of the main experimental parameters (gas pressures and voltages applied to the electrodes). The procedure by which Rydberg electron attachment was confirmed is described. A polychlorobiphenyl compound was used to illustrate the performance of this ionization technique. Ion formation was observed in the absence of fragmentation.

Gene mapping by linkage and association analysis.

Genetic analysis is used to map genes, including disease loci, to positions within the human genome. Linkage analysis depends on the co-segregation of a gene (locus) and a phenotype through a pedigree, while association analysis, or linkage disequilibrium mapping, depends on measuring deviation from the random occurrence of alleles in a haplotype in unrelated individuals or nuclear families. Complex computer programs may be used in both forms of analysis. In recent years most interest has focused on identifying genes involved in common, multifactorial diseases. Here I review some current and developing techniques of genetic analysis and give references to where further information can be obtained.

Susceptibility locus for IgA deficiency and common variable immunodeficiency in the HLA-DR3, -B8, -A1 haplotypes.

BACKGROUND: A common genetic basis for IgA deficiency (IgAD) and common variable immunodeficiency (CVID) is suggested by their occurrence in members of the same family and the similarity of the underlying B cell differentiation defects. An association between IgAD/CVID and HLA alleles DR3, B8, and A1 has also been documented. In a search for the gene(s) in the major histocompatibility complex (MHC) that predispose to IgAD/CVID, we analyzed the extended MHC haplotypes present in a large family with 8 affected members. MATERIALS AND METHODS: We examined the CVID proband, 72 immediate relatives, and 21 spouses, and determined their serum immunoglobulin concentrations. The MHC haplotype analysis of individual family members employed 21 allelic DNA and protein markers, including seven newly available microsatellite markers. RESULTS: Forty-one (56%) of the 73 relatives by common descent were heterozygous and nine (12%) were homozygous for a fragment or the entire extended MHC haplotype designated haplotype 1 that included HLA- DR3, -C4A-0, -B8, and -A1. The remarkable prevalence of haplotype 1 was due in part to marital introduction into the family of 11 different copies of the haplotype, eight sharing 20 identical genotype markers between HLA-DR3 and HLA-B8, and three that contained fragments of haplotype 1. CONCLUSION: Crossover events within the MHC indicated a susceptibility locus for IgAD/CVID between the class III markers D821/D823 and HLA-B8, a region populated by 21 genes that include tumor necrosis factor alpha and lymphotoxins alpha and beta. Inheritance of at least this fragment of haplotype 1 appears to be necessary for the development of IgAD/CVID in this family.

Mapping of 10 novel microsatellites in the MHC class III region: application to the study of autoimmune disease.

The MHC class III region contains many genes that are good candidates for involvement in autoimmune disease. We report the mapping and characterization of 10 novel (CA)n microsatellites spanning the region, which are highly informative and suitable for linkage and association studies. We used these markers to identify haplotypes of MHC class III microsatellite alleles in DNA from cell lines homozygous for MHC class II and class I alleles.

Gene ordering and localization by linkage analysis.

This chapter has covered the preparation of pedigree and datafiles suitable for linkage analysis, the calculation of gene frequencies and recombination fractions, the ordering of markers into a genetic map, and the placing of an unknown locus, such as a disease locus or phenotype, onto a fixed map of markers. The chapter has concentrated on the use of the GAS package, but some other programs for linkage analysis have also been mentioned.

The classical human phosphoglucomutase (PGM1) isozyme polymorphism is generated by intragenic recombination.

The molecular basis of the classical human phosphoglucomutase 1 (PGM1) isozyme polymorphism has been established. In 1964, when this genetic polymorphism was first described, two common allelozymes PGM1 and PGM1 2 were identified by starch gel electrophoresis. The PGM1 2 isozyme showed a greater anodal electrophoretic mobility than PGM1 1. Subsequently, it was found that each of these allelozymes could be split, by isoelectric focusing, into two subtypes; the acidic isozymes were given the suffix + and the basic isozymes were given the suffix -. Hence, four genetically distinct isozymes 1+, 1-, 2+, and 2- were identified. We have now analyzed the whole of the coding region of the human PGM1 gene by DNA sequencing in individuals of known PGM1 protein phenotype. Only two mutations have been found, both C to T transitions, at nt 723 and 1320. The mutation at position 723, which changes the amino acid sequence from Arg to Cys at residue 220, showed complete association with the PGM1 2/1 protein polymorphism: DNA from individuals showing the PGM1 1 isozyme carried the Arg codon CGT, whereas individuals showing the PGM1 2 isozyme carried the Cys codon TGT. Similarly, the mutation at position 1320, which leads to a Tyr to His substitution at residue 419, showed complete association with the PGM1+/- protein polymorphism: individuals with the + isozyme carried the Tyr codon TAT, whereas individuals with the - isozyme carried the His codon CAT. The charge changes predicted by these amino acid substitutions are entirely consistent with the charge intervals calculated from the isoelectric profiles of these four PGM1 isozymes. We therefore conclude that the mutations are solely responsible for the classical PGM1 protein polymorphism. Thus, our findings strongly support the view that only two point mutations are involved in the generation of the four common alleles and that one allele must have arisen by homologous intragenic recombination between these mutation sites.

Genetic polymorphism in the 3' untranslated region of human phosphoglucomutase-1.

A 317-bp segment of DNA from the 3' region of the human phosphoglucomutase-1 (PGM1) gene has been examined by a non-radioactive technique for the occurrence of single-strand conformation polymorphism (SSCP). Eight phenotypes were detected and attributed to the presence of four alleles. Genetic analysis of 75 unrelated individuals and six CEPH families whose PGM1 protein phenotypes were known revealed strong association between the PGM1 '+' and '-' isozyme phenotypes and the variation detected in this region, but no association with the PGM1 1 and PGM1 2 isozyme phenotypes. DNA sequence analysis demonstrated the presence of three nucleotide substitutions underlying the alleles, which were located in the untranslated region of the PGM1 gene. There was complete correlation between the nucleotide sequence and the phenotype detected by SSCP analysis. This study provides support for the model that the PGM1 isozyme polymorphism is determined at two distinct sites in the coding sequence, one coding for the '1' and '2' alleles and the other coding for the '+' and '-' alleles, separated by a region where intragenic recombination occurs.

Computer simulation of single-ion trajectories in paul-type ion traps.

The computer simulation of single-ion trajectories using a number of computer programs is described together with associated theory. The programs permit calculation of ion trajectories while the ion is subjected to collisions with buffer gas of variable pressure, resonance excitation in any of three modes, and static or ramped DC and radiofrequency levels. Initially, the programs were designed for the calculation of ion trajectories in a quadrupole ion trap. The programs now permit such calculations for ions confined in traps having electrodes shaped to include percentages of hexapole and octupole components in the electric field as well as electrode surface geometries for which there is no closed-form expression. The Langevin collision theory is reviewed and a theoretical treatment of the multipole trap is presented.

Identification of eight coumarins occurring with psoralen, xanthotoxin, and bergapten on leaf surfaces.

Surface extracts of the leaves of five species in the Umbelliferae,Citrus limon (Rutaceae), andPsoralea bituminosa (Leguminosae) were examined for the presence of coumarins, after a previous study had shown the presence of three psoralens. In the current investigation eight more coumarins were identified by mass spectrometric techniques: the simple coumarins scopoletin, scoparone, and osthol, the linear furanocoumarins imperatorin and phellopterin, the angular furanocoumarins angelicin and pimpinellin, and the pyranocoumarin seselin. Five of these occur inApium graveolens, and scopoletin, scoparone, and imperatorin were each found in three of the species examined. The co-occurrence of all these coumarins on the surface may be significant in communication between the plant and its environment.

IgM, IgG and IgA rheumatoid factors (antiglobulins) in early rheumatoid arthritis and their production of articular index over one year.

An enzyme-linked immunosorbent assay was used to detect antiglobulins (rheumatoid factors, RF) of various classes in 33 patients with recently diagnosed rheumatoid arthritis and to follow their progress with 3-monthly checks for 1 year. For RF, IgA-RF and IgM-RF showed greater sensitivity than the latex test, either or both being positive in 76%. There was no correlation between any of the measures of RF and patient's clinical status as judged by articular index (AI), or serum CRP level. For individual patients, RF levels varied considerably between assessments. The best predictors of clinical status over 1 year were the initial AI and the latex test for RF. While class-specific measurement of RF is more sensitive than the latex test, the variation of individual classes of antiglobulins over time within individual patients makes them less helpful as predictors of disease progress.