High-throughput next-generation sequencing to genotype six classical HLA loci from 96 donors in a single MiSeq run.

Next generation sequencing (NGS) methods have been established as an efficient approach for HLA typing because unlike traditional Sanger sequencing, they provide unambiguous results at a reasonable cost. We previously developed a multi-locus index method to genotype four HLA loci (A, B, C, and DRB1) on the Illumina MiSeq platform. We have now expanded this method to include two additional loci, HLA-DPB1 and DQB1. Contiguous full-length amplicons from 5'UTR through 3'UTR regions were generated using one long-range PCR reaction per locus for each of the six loci from 96 individuals of different ethnicities. The six amplicons from each donor were pooled, enzymatically fragmented and given a donor-specific index. This approach enabled sequencing of 576 loci from 96 individuals in a single MiSeq run. Donor-specific sequence reads were demultiplexed, and allele calls were generated from FASTQ files using commercially available software. Comparison to HLA genotypes generated from Sanger sequence-based typing (SBT) identified no discordances among any of the alleles analyzed in this study. Importantly, this method was able to resolve 22 DPB1 and 20 DQB1 alleles that were ambiguous with the SBT method. Furthermore, a novel allele in each of these two loci was identified, with the DQB1*05:01:24 allele having a frequency of greater than five percent. This method was subsequently validated against a blinded panel of 22 samples from the 17th International HLA and Immunogenetics Workshop. The flexibility of the method is further highlighted by successful genotyping of eight loci comprising all classical HLA loci for a subset of the samples. We now present a high-throughput, high-resolution, scalable NGS HLA typing method to accurately and efficiently genotype all classical HLA class I and II loci.

Induction of cytochrome P4501A1 by photooxidized tryptophan in Hepa lclc7 cells.

Mouse hepatoma Hepa-lclc7 (Hepa-1) cells were cultivated in the presence of UV-irradiated amino acids. The results demonstrated that all of the amino acids tested, UV-oxidized tryptophan caused the highest induction of 7-ethoxyresorufin O-deethylase (EROD) activity compared with the controls (P < 0.01). The induction of EROD activity by oxidized tryptophan was dose dependent, and maximal induction was obtained at 12 hr after administration. Studies with various Hepa-1 mutants, which are defective in either the aryl hydrocarbon (Ah) receptor or Ah receptor nuclear translocator protein, indicated that the induction of EROD activity by oxidized tryptophan occurs through the Ah receptor. Gel mobility shift assays using nuclear extracts of Hepa-1 cells revealed that oxidized products of tryptophan can induce both Ah receptor transformation and binding of the liganded Ah receptor complex to its specific DNA recognition site. CYP1A1 mRNA, quantified by reverse transcription-polymerase chain reaction, and CYP1A1 protein were induced markedly in the oxidized tryptophan group compared with the controls. Injection of isolated oxidized tryptophan products into adult male rats caused significant induction of EROD activity in the pulmonary and hepatic microsomes compared with the controls (P < 0.01). These results demonstrated that oxidized tryptophan induces Ah receptor activation and binding of the liganded Ah receptor complex to its specific DNA recognition site, thereby initiating transcription and translation of the CYP1A1 gene with concomitant increase of EROD activity in Hepa-1 cells. Induction of EROD activity in the liver and lungs after injection of isolated oxidized tryptophan products into rats suggests that a similar mechanism may be operative in vivo.

Effect of pyridoxine deficiency on Litomosoides carinii infection in albino rats.

Pyridoxine deficiency has been induced in albino rats at the weanling or neonatal stages. Exposure of the vitamin-deficient rats to the infective larvae of Litomosoides carinii resulted in no development or establishment of the parasite in the host. Although the food consumption of the pair-fed group was necessarily restricted to that of the deficient group, the susceptibility of the animals of the pair-fed group receiving the normal vitamin intake resembled that of the control group. The humoral immune response to the infection in the pair-fed controls as measured by indirect haemagglutination, was inhibited compared to that in the controls. This inhibition was more severe in the vitamin-deficient animals.

Immunogenicity of homogenates of the developmental stages of Litomosoides carinii in albino rats.

Homogenates of different developmental stages of the filarial parasites, L. carinii, emulsified in Freund's complete adjuvant have been examined for their efficacy in conferring immunity to the infection in the albino rats. The results revealed that sonicated preparations of microfilariae and infective larvae induce high resistance to the infection in the animals. In contrast, soluble antigens of adults and sonicated homogenates of adult males were ineffective to induce such resistance. Some resistance seen when sonicated adult worms of both sexes were used as immunogens appears to be due to the microfilarial antigen present in the extracts.

Differential effect of interleukin-1 alpha on rat hepatic cytochrome P450 monooxygenases.

Administration of recombinant human interleukin-1 alpha to adult male rats caused a significant reduction in the levels of hepatic cytochrome P450 and P450 reductase activity at 24 h after the treatment. The mRNAs for cytochrome P450 1A2 and 2E1 were reduced more than 70% at 12 h after administration of interleukin-1 alpha and remained decreased even after 48 h. By contrast, cytochrome P450 2C11 mRNA was reduced only by 30% at 12 h after the treatment and returned to the control levels by 48 h, suggesting that interleukin-1 alpha has a differential effect on the expression of P450 mRNAs. Aniline hydroxylase, benzphetamine N-demethylase and 7-ethoxycoumarin O-deethylase activities were significantly decreased at 24 h after interleukin-1 alpha treatment. The proteins for cytochrome P450 1A2 and 2E1 were reduced by about 50% at 24 h after interleukin-1 alpha treatment.

Metabolism of (+)-trans-benzo[a]pyrene-7,8-dihydrodiol by 3-methylcholanthrene-induced rat liver homogenates.

Using a new sensitive reverse-phase HPLC assay with on-line radioactivity detector, metabolism of (+)-trans-benzo[a]pyrene-7,8-dihydrodiol (B[a]P diol) to the ultimate carcinogen benzo[a]pyrene-7,8-diol-9,10-epoxide (B[a]PDE) was studied using 3-methylcholanthrene-induced rat liver homogenates. The results demonstrate that the stereoselectivity of B[a]PDE formation is a function of the concentration of the cellular constituents in the incubation media. At more dilute concentrations of the homogenate, the ratio of anti- to syn-B[a]PDE was the highest and decreased as the homogenate protein was increased in the incubation medium. However, there was a marked and parallel decrease of free B[a]PDE and DNA-bound radioactivity with increasing concentrations of cellular constituents in the incubation medium. The decreased DNA-bound radioactivity appears to be due to the preferential binding of B[a]PDE to glutathione and to proteins as the homogenate concentration was increased in the incubation media. These results indicate that liver homogenates, while apparently preserving the function of microsomes, present additional opportunities to study the interrelationship among cytochrome P450 monooxygenase activity, water-soluble conjugates, and binding of B[a]P diol metabolites to macromolecules in the study of benzo[a]pyrene-induced carcinogenesis.

Depression of hepatic cytochrome P450 monooxygenases after chronic environmental tobacco smoke exposure of young ferrets.

Six-week-old ferrets were exposed head-only to clean air or environmental tobacco smoke (ETS) for 2 h/day, 5 days a week for a total of 8 weeks. Exposure to ETS caused a significant reduction in the levels of hepatic microsomal cytochrome P450 and P450 reductase activity in both the male and female ferrets. The content of cytochrome b5 and the activity of its reductase were significantly reduced in the hepatic microsomes of female ferrets. 7-Ethoxycoumarin O-deethylase activity and cytochrome P450 (CYP) 1A protein were markedly decreased in the hepatic microsomes of both the male and female ferrets after ETS exposure. In accord with the downregulation of P450, total metabolites formed from benzo[a]pyrene were significantly reduced in the liver homogenates of ETS-exposed animals. Similarly, sum total of free (+)-anti-benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide, glutathione conjugates and DNA-bound metabolites formed from precursor (-)-7R-trans-benzo[a]pyrene-7,8-dihydrodiol showed marked reduction in both the male and female ferrets after ETS exposure in a dose-response manner. This is the first report showing downregulation of hepatic P450 and accompanying benzo[a]pyrene metabolism after tobacco smoke exposure which apparently occurred after an initial upregulation of these parameters (Rasmussen et al. (1994) FASEB J. 8, A122).

Induction of cytochrome P4501A1 by ozone-oxidized tryptophan in Hepa lclc7 cells.

The present investigation was undertaken to determine whether administration of O3-oxidized amino acids to mouse hepatoma cells, Hepa lclc7 (Hepa-1), in culture would effect Cyp1a1 gene expression. The results demonstrate that, of all the amino acids tested, only O3-oxidized tryptophan caused a significant induction of CYP1A1-dependent 7-ethoxyresorufin O-deethylase (EROD) activity compared to the controls (p < 0.01). CYP1A1 mRNA and protein were markedly induced in the O3-oxidized tryptophan administered group compared to the controls. Gel mobility shift assays using nuclear extracts of Hepa-1 cells revealed that oxidized products of tryptophan can induce both aryl hydrocarbon receptor (AhR) transformation and binding of the liganded AhR complex to its specific DNA recognition site, thereby initiating transcription of the Cyp1a1 gene with concomitant increase of CYP1A1 protein and EROD activity in Hepa-1 cells.

Conversion of xanthoxin to abscisic Acid by cell-free preparations from bean leaves.

Cell-free extracts from the leaves of Phaseolus vulgaris L. convert xanthoxin to abscisic acid. The enzyme activity in dialyzed or acetone-precipitated extracts shows a strong dependence on either NAD or NADP. The enzyme activity appears to be cytosolic with no significant activity observed in chloroplasts. The activity was observed in extracts from roots of Phaseolus vulgaris, and also in extracts prepared from the leaves of Pisum sativum L., Zea mays L., Cucurbita maxima Duchesne, and Vigna radiata L. Neither water stress nor cycloheximide appear to significantly affect the level of enzyme activity in leaves. No intermediates between xanthoxin and abscisic acid were detected.

Xanthoxin Metabolism in Cell-free Preparations from Wild Type and Wilty Mutants of Tomato.

Extracts prepared from the turgid and water-stressed leaves of wild-type tomato (Lycopersicon esculentum Mill cv Ailsa Craig) and the wilty mutants sitiens, notabilis, and flacca were tested for their ability to metabolize xanthoxin to ABA. Extracts from wild type and notabilis converted xanthoxin at similar rates, while extracts from sitiens and flacca showed little or no activity. We also observed no activity when extracts of sitiens and flacca were mixed. Similar results were obtained when ABA aldehyde was used as a substrate, in that extracts from wild type and notabilis were equally active, but extracts from flacca and sitiens showed little activity. None of the tomato extracts showed significant activity with xanthoxin acid, xanthoxin alcohol, or ABA-1',4-'Trans-diol as substrates. Extracts from bean leaves (Phaseolus vulgaris L. cv Blue Lake) were similar to the wild-type tomato extracts in their ability to convert the various substrates to ABA, although excised bean leaves did convert ABA-1',4'-trans-diol and xanthoxin alcohol to ABA when these substances were taken up through the petiole. These results are consistent with a role for xanthoxin as a normal intermediate on the ABA biosynthetic pathway, and they suggest that ABA aldehyde is the final ABA precursor.

Propylamine transferases in chinese cabbage leaves.

We have found spermidine synthase and spermine synthase activities in extracts of leaves of Chinese cabbage (Brassica pekinensis var. Pak Choy) and have developed an assay of the former in crude extracts. The method is based on the transfer of the propylamine moiety of decarboxylated S-adenosylmethionine to labeled putrescine, followed by ion-exchange separation of the labeled amine substrate and product, which are then converted to the 5-dimethylamino-1-napthalene sulfonyl (dansyl) derivatives and further purified and identified by thin layer chromatography. The specific radioactivity of putrescine present in the reaction mixture is determined, as is the radioactivity present in dansyl spermidine. The enzyme is also present in extracts of spinach leaves.Spermidine synthase has been purified about 160-fold from Chinese cabbage leaves. After partial purification, a rapid coupled enzymic assay has been used to study various properties of the enzyme. The plant enzyme shows maximum activity at pH 8.8 in glycine-NaOH buffer and has a molecular weight of 81,000. The K(m) values for decarboxylated S-adenosylmethionine and putrescine are 6.7 and 32 micromolar, respectively. The enzyme activity is inhibited strongly by dicyclohexylamine, cyclohexylamine, and S-adenosyl-3-thio-1, 8-diaminoctane. Of these, dicyclohexylamine is the most potent inhibitor with an I(50) at 0.24 micromolar.

Subcellular localization of spermidine synthase in the protoplasts of chinese cabbage leaves.

Previous studies on the presence of spermidine synthase (EC 2.5.1.16) in the protoplasts of Chinese cabbage (Brassica pekinensis var Pak Choy) leaves had detected a small but significant fraction of the enzyme in a crude chloroplast fraction (Cohen, Balint, Sindhu 1981 Plant Physiol 68: 1150-1155). To establish whether this enzyme is truly a chloroplast component, we have isolated purified intact chloroplasts from protoplasts by density gradient centrifugation in silica sols (Ludox AM). Such chloroplasts contained all of the diaminopimelate decarboxylase (EC 4.1.1.20) of the protoplasts, but were essentially devoid of spermidine synthase. Control experiments showed that the latter had not been inactivated under conditions of isolation, purification, and assay of the intact chloroplasts. Isolation and assay of protoplast vacuoles in a further examination of the supernatant fluid containing the enzyme revealed a significant fraction of the enzyme in the vacuole fraction. However this fraction was found to contain similar proportions of a soluble enzyme, glucose 6-phosphate dehydrogenase. It has been concluded that vacuolar fractions are difficultly separable from soluble cytoplasmic material, which is probably the only compartment containing spermidine synthase.

Agmatine iminohydrolase activity during development and germination of groundnut seeds.

During the development of groundnut seeds agmatine iminohydrolase activity increased in the cotyledons but remained constant in the embryo. In seeds stored for 1 year, decreased activity of the enzyme was found in both cotyledons and embryo. During germination, the enzyme activity increased in the cotyledons, but in the embryo it increased up to day 3 and then decreased to the initial level.

Effect of phytic acid on diamine oxidase activity in germinating pea seeds.

Diamine oxidase present in the cotyledons of germinating pea seeds is induced by phytic acid but the embryo enzyme is not affected. Polyamines have no effect on phytase activity of the cotyledon or embryo.

Induction of cytochrome P-450 1A2 by oxidized tryptophan in Hepa lclc7 cells.

Recent studies from this laboratory have demonstrated that L-tryptophan, after oxidation either by UV-irradiation or ozone, induces aryl hydrocarbon receptor (AhR) activation and binding of the liganded AhR complex to its specific DNA recognition site, thereby initiating transcription of the cytochrome P-450 1a1 (Cyp1a1) gene with concomitant increase of CYP1A1 protein and 7-ethoxyresorufin O-deethylase activity in wild-type mouse hepatoma cells, Hepa lclc7 (Hepa-1), in culture. Temporary inhibition of protein synthesis by cycloheximide resulted in superinduction of oxidized tryptophan-inducible CYP1A1 mRNA, protein, and 7-ethoxyresorufin O-deethylase activity in Hepa-1 cells. In the present communication, the results obtained by immunoblot analyses with monoclonal CYP1A1/1A2 antibody (NIH 1-7-1) demonstrate that both UV- or ozone-oxidized tryptophan also induce CYP1A2 protein in Hepa-1 cells. CYP1A2 mRNA, detected by reverse transcription-polymerase chain reaction, was markedly induced in the UV- or ozone-oxidized tryptophan-treated cells. Temporary inhibition of protein synthesis by cycloheximide further induced oxidized tryptophan-inducible CYP1A2 mRNA as well as the protein in Hepa-1 cells. This is the first report demonstrating the induction of CYP1A2 mRNA and protein in Hepa-1 cells.

Undernutrition during hyperoxic exposure induces CYP2E1 in rat liver.

Induction of cytochrome P450 2E1 (CYP2E1) has been shown to occur through two distinct mechanisms. The first is seen by treatment of rats with acetone, pyrazole, and 4-methyl-pyrazole, which induces CYP2E1 protein without affecting the mRNA level. The second is observed in starvation, diabetes, and obesity, in which an increase of CYP2E1 protein is associated with an increase of the CYP2E1 mRNA. It has been reported by (Tindberg and Ingelman-Sundberg 1989) that hyperoxic exposure (95% O2) induced a several-fold increase of CYP2E1 protein in both the liver and lung of exposed rats without affecting the level of CYP2E1 mRNA. During the course of our previous study which demonstrated hyperoxia-induced specific pretranslational induction of CYP1A1/2 in the liver and CYP1A1 in the lung, we observed a progressive increase of hepatic CYP2E1 mRNA in animals of the hyperoxia group. Hyperoxia is accompanied by some degree of starvation and our earlier experiments were conducted with rats of significantly greater body weight than those used by Tindberg and Ingelman-Sundberg (260 vs 150 g). Thus we reevaluated the changes of CYP2E1 in the current study with the use of food-restricted control, and by utilizing rats of comparable weight (approximately 150 g) to that utilized by Tindberg and Ingelman-Sundberg. The results obtained in the present study showed that there was a significant increase in the levels of hepatic CYP2E1 mRNA, protein, and p-nitrophenol hydroxylase activity in the food-restricted control group compared to the untreated controls. Rats from the hyperoxia group also demonstrated a similar increase of these three parameters in their livers but showed no significant difference compared with the results of the food-restricted control group. Rats weighing approximately 260 g were also examined with similar food restriction and hyperoxia, and the results were essentially similar to those obtained with the younger rats. The lungs of rats from food-restricted control and hyperoxia groups showed no increase of any of the CYP2E1 parameters. The results obtained in the current study, therefore, indicate that hyperoxia has no effect on CYP2E1 expression in both the liver and lung. Increased CYP2E1 mRNA, protein, and p-nitrophenol hydroxylase activity seen in the liver of rats, but not in the lungs, are consistent with the notion that undernutrition during hyperoxia is the underlying mechanism for this induction.

The synthesis of polyamines from methionine in intact and disrupted leaf protoplasts of virus-infected chinese cabbage.

In exploring the role of the chloroplast in the multiplication of turnip yellow mosaic virus, the biosyntheses of the major viral polyamine, spermidine, as well as that of the tetramine, spermine were studied. The synthesis of these polyamines from [2-(14)C]methionine in protoplasts of Chinese cabbage leaf cells derived from healthy plants or those infected by turnip yellow mosaic virus were examined. Populations of protoplasts of infected leaves are homogeneous with respect to containing chloroplast aggregates in contrast to those of healthy leaves. Protoplast preparations have been shown to incorporate methionine into protein, spermidine, and spermine more rapidly than do fresh leaf discs, which also show a very slow utilization of labeled arginine and ornithine into polyamine.Protein synthesis is similar for 4 hours in both healthy and infected protoplasts. Accumulation of labeled spermidine stops after 2 hours in healthy protoplasts but continues in the infected protoplasts. Much of the newly synthesized protein and spermidine is present in the easily sedimentable fraction of the readily disrupted protoplasts.Disrupted and diluted protoplasts have a decreased ability to metabolize methionine to protein and spermidine. The residual synthetic activity is essentially entirely in the easily sedimentable fraction. However, this fraction is unable to synthesize spermine, an activity found in protoplasts and disrupted protoplasts. Disrupted protoplasts contain spermidine synthase (EC 2.5.1.16) and about a quarter of this activity is present in a low-speed sedimentable fraction containing the chloroplasts. The protoplast system is suitable for an analysis of polyamine synthesis in turnip yellow mosaic virus infection and appears particularly suitable for study of the distribution of the enzymes involved.

Chronic exposure to ozone and nitric acid vapor results in increased levels of rat pulmonary putrescine.

In the past decade, there has been growing public concern for the human health effects of exposure to environmental pollutants. Ozone (O3) is one of the most reactive components of photochemical air pollution. Despite extensive investigations by many laboratories on the functional, biochemical, and cellular effects of O3 exposure in humans, animals, and in vitro systems, questions remain concerning the potential adverse effects to human health represented by chronic near-ambient exposure to this environmental pollutant. In the present investigation, the influence of inhalation of O3 and nitric acid (HNO3) vapor on polyamine levels was examined in rat lungs. Male F344/N rats were exposed nose-only to 0.15 ppm O3 and 50 microg/m3 HNO3 vapor alone and in combination for 4 hours/day. 3 days/week for a total of 40 weeks. At this time the animals were sacrificed and their lungs were examined for polyamine contents. Exposure to O3 and O3 plus HNO3 vapor caused a significant increase in the putrescine content of the lung compared to the air-exposed controls (P < 0.05). The concentrations of pulmonary spermidine and spermine were not significantly increased by exposure to either O3 or HNO3 vapor alone or in combination compared to the air-exposed controls. The role of polyamines in repair and anti-inflammatory processes has been discussed.

Abscisic Aldehyde Is an Intermediate in the Enzymatic Conversion of Xanthoxin to Abscisic Acid in Phaseolus vulgaris L. Leaves.

The enzymatic conversion of xanthoxin to abscisic acid by cell-free extracts of Phaseolus vulgaris L. leaves has been found to be a two-step reaction catalyzed by two different enzymes. Xanthoxin was first converted to abscisic aldehyde followed by conversion of the latter to abscisic acid. The enzyme activity catalyzing the synthesis of abscisic aldehyde from xanthoxin (xanthoxin oxidase) was present in cell-free leaf extracts from both wild type and the abscisic acid-deficient molybdopterin cofactor mutant, Az34 (nar2a) of Hordeum vulgare L. However, the enzyme activity catalyzing the synthesis of abscisic acid from abscisic aldehyde (abscisic aldehyde oxidase) was present only in extracts of the wild type and no activity could be detected in either turgid or water stressed leaf extracts of the Az34 mutant. Furthermore, the wilty tomato mutants, sitiens and flacca, which do not accumulate abscisic acid in response to water stress, have been shown to lack abscisic aldehyde oxidase activity. When this enzyme fraction was isolated from leaf extracts of P. vulgaris L. and added to extracts prepared from sitiens and flacca, xanthoxin was converted to abscisic acid. Abscisic aldehyde oxidase has been purified about 145-fold from P. vulgaris L. leaves. It exhibited optimum catalytic activity at pH 7.25 in potassium phosphate buffer.

Neonatal hyperoxia and cytochrome P450 imprinting in adulthood.

We hypothesized that during a critical neonatal period hyperoxia may produce alterations of sex-specific cytochrome P450 isozymes in adulthood (enzyme imprinting). To test this, newborn rats were exposed to 24 or 72 h of hyperoxia (O2 > 95%) within 24 h after birth and killed at 120 d. In males, significant negative imprinting (decrease) was found in total cytochrome P450 content and male-specific CYP2C11 in the hyperoxia groups. Positive imprinting (increase) was noted in CYP1A2 and male-specific CYP3A2 in the 72-h hyperoxia group. These alterations were essentially similar when expressed on a per microsomal protein or per liver basis. In addition, the level of hepatic glucocorticoid receptor in adult male rats was elevated after neonatal hyperoxia. In females, there was a significant body and liver weight loss after hyperoxic exposure, which resulted in a negative imprinting of CYP1A2 and female-specific 2C12 in the 72-h hyperoxia group on a per liver basis, whereas the measured parameters were unaltered when expressed per microsome. In general, the changes were more marked with longer hyperoxic exposure, suggesting that more pronounced alterations may be induced with prolonged neonatal hyperoxia. Because hyperoxic exposure in premature neonates is a common clinical practice and decreased CYP2C11 in adult males is expected to result in feminization, we believe that the scope of this work should be expanded and eventually tested for its relevance in human subjects.