Estimation of the average burst size of Phix174 am3, cs70 for use in mutation assays with transgenic mice

In mutation assays using transgenic mice, with recoverable vectors such as PhiX174 am3, cs70, mutations originate from two sources: (1) in vivo mutations, that is, mutations that were fixed in the mouse, or (2) ex vivo mutations, that is, mutations that were fixed during recovery or plating. When a bacteriophage infects a bacterium, it multiplies and bursts the cell, releasing a number of phages referred to as the burst size. Our method for distinguishing between in vivo mutations and ex vivo mutations estimates the average number of bursts, the denominator of in vivo mutant frequencies, by dividing the total plaque-forming units (PFU) by the average number of phages in a burst. Herein, we outline a probability model relating observed plaque counts to the burst size and present the statistical method used to estimate the burst size. The average size of a single burst from nonrevertant phages was estimated in eight studies under the conditions of our mutation assay. The average burst size was stable across studies at 182.5 plaques per burst (standard error, 14.25). The probability that a burst is a specific size was approximated by a negative binomial distribution, which implies a Poisson-Pascal distribution for the observed plaque counts. The observed plaque counts were adequately fit by this approximation. Environ. Mol. Mutagen. 37:356-360, 2001 Published 2001 Wiley-Liss, Inc.

Predicted changes in pre-mRNA secondary structure vary in their association with exon skipping for mutations in exons 2, 4, and 8 of the Hprt gene and exon 51 of the fibrillin gene

Exon skipping that accompanies exonic mutation might be caused by an effect of the mutation on pre-mRNA secondary structure. Previous attempts to associate predicted secondary structure of pre-mRNA with exon skipping have been hindered by either a small number of available mutations, sub-optimal structures, or weak effects on exon skipping. This report identifies more extensive sets of mutations from the human and hamster Hprt gene whose association with exon skipping is clear. Optimal secondary structures of the wild-type and mutant pre-mRNA surrounding each exon were predicted by energy minimization and were compared by energy dot plots. A significant association was found between the occurrence of exon skipping and the disruption of a stem containing the acceptor site consensus sequences of exon 8 of the human Hprt gene. However, no change in secondary structure was associated with skipping of exon 4 of the hamster Hprt gene. Using updated energy parameters we found a different structure than that previously reported for exon 2 of the hamster Hprt gene. In contrast to the previously reported structure, no significant association was found between predicted structural changes and skipping of exon 2. For all three Hprt exons studied, there was a significantly greater number of deoxythymidine substitutions among mutations accompanied by exon skipping than among mutations without exon skipping. For exon 8, deoxythymidine substitution was also associated with structural changes in the stem containing the acceptor site consensus sequences. For exon 51 of the human fibrillin gene, structural differences from wild type were predicted for all four mutations accompanied by exon skipping that were not were predicted for a single mutation without exon skipping. Our results suggest that both primary and secondary pre-mRNA structure contribute to definition of Hprt exons, which may involve exonic splicing enhancers.

The association of nonsense codons with exon skipping

Some genes that contain premature nonsense codons express alternatively-spliced mRNA that has skipped the exon containing the nonsense codon. This paradoxical association of translation signals (nonsense codons) and RNA splicing has inspired numerous explanations. The first is based on the fact that premature nonsense codons often reduce mRNA abundance. The reduction in abundance of full-length mRNA then allows more efficient amplification during PCR of normal, minor, exon-deleted products. This mechanism has been demonstrated to explain an extensive correlation between nonsense codons and exon-skipping for the hamster Hprt gene. The second explanation is that the mutation producing an in-frame nonsense codon has an effect on exon definition. This has been demonstrated for the Mup and hamster Hprt gene by virtue of the fact that missense mutations at the same sites also are associated with the same exon-deleted mRNA. The third general explanation is that a hypothetical process takes place in the nucleus that recognizes nonsense codons, termed 'nuclear scanning', which then has an effect on mRNA splicing. Definitive evidence for nuclear scanning is lacking. My analysis of both nonsense and missense mutations associated with exon skipping in a large number of genes revealed that both types of mutations frequently introduce a T into a purine-rich DNA sequence and are often within 30 base pairs of the nearest exon boundary. This is intriguing given that purine-rich splicing enhancers are known to be inhibited by the introduction of a T. Almost all mutations associated with exon skipping occur in purine-rich or A/C-rich sequences, also characteristics of splicing enhancers. I conclude that most cases of exon skipping associated with premature termination codons may be adequately explained either by a structural effect on exon definition or by nonquantitative methods to measure mRNA, rather than an effect on a putative nuclear scanning mechanism.

The association of nonsense mutation with exon-skipping in hprt mRNA of Chinese hamster ovary cells results from an artifact of RT-PCR

RT-PCR of RNA from CHO cells with nonsense mutations in the hprt gene frequently detects minor hprt mRNA species lacking one or more exons. Many nonsense mutants also contain greatly reduced concentrations of the major, normally spliced hprt mRNA. In this study, we examined the hypothesis that exon-deleted mRNAs are normal constituents of CHO cells, but are not detected in wild-type parental cells and most missense mutants because their amplification is suppressed by relatively high concentrations of normally spliced hprt mRNA. A protocol designed to specifically detect exon-deleted mRNAs was conducted using RNA from parental cells and identified all the exon-deleted species typical of nonsense mutants. Quantitative analysis of parental cell RNA measured these exon-deleted mRNAs at < or = 0.7% of the abundance of the full-sized species. Nonsense and missense mutants had comparable amounts of exon-deleted mRNAs, which varied both above and below parental concentrations. The relative concentrations of particular exon-deleted species could be explained by the location of nonsense mutations remaining in the mRNA or by structural effects of mutations on splicing. Exon-deleted mRNAs were detected by RT-PCR when the concentration of the most abundant exon-deleted species was > or = 2% of the full-length mRNA. This occurred for mutants with nonsense mutations in internal exons. RT-PCR conditions were shown to suppress the amplification of exon-deleted species 40-fold when full-length mRNA was abundant, which occurred for parental lines and missense mutants. Our results verify that RT-PCR conditions can produce an artifactual association between nonsense mutation and exon-skipping when minor, exon-deleted mRNA is relatively enriched.

The use of transgenic cell lines for evaluating toxic metabolites of carbamazepine

Human lymphoblastoid cell lines transgenic for human CYP450s were evaluated for the identification of toxic metabolites of the anticonvulsant drug carbamazepine (CBZ). Human CYP450 isoforms expressed by these cell lines included 1A1, 1A2, 2E1, 2A6, and 3A4. A dose-dependent inhibition of population growth from 50-200 micrograms/ml CBZ was detected by measuring cell number and respiration. The inhibition increased with the growth rate of the various lines, which correlated inversely with the presence of CYP450s, and may have been caused by CBZ itself. Cytotoxicity was observed only at the highest dose and in the line lacking transfected CYP450s. Microsomal preparations from hCYP3A4/OR cells converted CBZ into its principal oxidative metabolite, carbamazepine-10,11-epoxide (CBZ-E), at a rate of 630 pmol/min per mg protein, confirming a major role of CYP3A4 in this reaction. However, no CBZ-E (or any metabolite) was recovered from any whole-cell incubation even though hCYP3A4 cells readily converted testosterone to 6 beta-hydroxytestosterone. This suggests that differences exist between whole-cell and microsomal preparations of lymphoblastoid cells in their ability to metabolize CBZ.

GC-MS determination of amphetamine and methamphetamine in human urine for 12 hours following oral administration of dextro-methamphetamine: lack of evidence supporting the established forensic guidelines for methamphetamine confirmation

Ten human volunteers, naive to amphetamines and divided into two groups of five each, were given an oral dose of 30 mg/70 kg D-methamphetamine in one of two different paradigms: the initial dose at 0930 h or the initial dose at 2130 h. One week later, each subject was crossed over with regard to time but given the same dose. A total of 214 urine specimens were collected either prior to dosing or at each micturition for a 12-h period post dose. Specimens were analyzed on a blind basis for methamphetamine and one of its metabolites, amphetamine, by gas chromatography-mass spectrometry (GC-MS) using coinjection of extracted sample and pentafluoropropionic anhydride and selected-ion monitoring. Approximately 20% of the D-methamphetamine was recovered unchanged from the urine specimens, and 2% was recovered as amphetamine. The mean urine methamphetamine concentration in both groups reached a maximum within 4-6 h and declined thereafter. A residual amount of methamphetamine was found in some predose specimens at the crossover evaluation, reflecting that methamphetamine may be detected in urine for up to 7 days. The amphetamine concentration reached a plateau by 4-6 h. This observation coupled with the finding that all subjects excreted approximately 2% of the methamphetamine dose as amphetamine suggested a saturable process for its biotransformation. Concentrations of both methamphetamine and amphetamine tended to be higher, but were not significantly different, for night administration. Methamphetamine concentrations were consistently greater than the 500-ng/mL cutoff in most post-dosing specimens, whereas amphetamine concentrations generally did not achieve the 200-ng/mL cutoff specified by the Substance Abuse and Mental Health Services Administration (SAMHSA) guidelines for GC-MS confirmation of methamphetamine. Some specimens containing methamphetamine had no amphetamine metabolite. The current guidelines would have resulted in 90.2% of the specimens containing methamphetamine being ruled negative by confirmation following either night or day administration, whereas one subject following the initial day administration and another following night crossover administration would have been judged positive at most time intervals. These findings suggest that the current SAMHSA guidelines select for individual metabolic variations and that GC-MS confirmation of methamphetamine will result in most occasional users being ruled negative following an oral dose of methamphetamine while some will be ruled positive.

Genomic DNA sequencing of mRNA splicing mutants in the hprt gene of Chinese hamster ovary cells

We have analyzed 41 mRNA-splicing mutants from the hypoxanthine-guanine phosphoribosyl-transferase (hprt) gene of Chinese hamster ovary (CHO) cells. Twenty-two of these mutants produced single cDNA PCR products with a partial or complete exon deletion; 19 mutants produced multiple cDNA PCR products, and most of these products contained one or more deleted exons. The affected exons and surrounding introns were amplified from genomic DNA and sequenced in order to identify mutations causing aberrant splicing. We found acceptor site mutations in 10 mutants, exonic mutations in 8 mutants, and no mutations in 5 mutants. Four mutants from solvent controls did not amplify the appropriate exons and were considered genomic deletion mutants. Our previous work [Manjanatha MG et al. (1994): Mutat Res 308;65-75] showed that nonsense mutants in the hprt gene of CHO cells are associated with multiple cDNA PCR products containing deleted exons and a low abundance of hprt mRNA if the mutation is found in an internal exon. The present results are consistent with these associations being facilitated by instability of mRNA after ribosome termination at nonsense codons.

DNA sequence of direct repeats of the sulI gene of plasmid pSa

The restriction enzyme and genetic map of the antibiotic-resistance region of plasmid pSa is related to Tn21 integrons by the insertion of 5.4 kb containing a chloramphenicol resistance gene (catII) and a 1.1-kb direct repeat. We report here the nucleotide sequences of both copies of the repeat with adjoining sequences. They were identical for 1065 bp and contained the entire coding sequence of the sulfanilamide resistance gene, sulI. Since only the first copy of the repeat confers sulfonamide resistance, this leads to the conclusion that no promoter was available for the second copy. The sequence of the pSa sulI gene was identical to several published sulI sequences from other plasmids. The first junction point of the catII-containing insert was identical to the sequence for pDG0100; the second junction occurred farther into the 3'-conserved segment of integrons than does that of pDG0100. A recent report of these junction sequences for pSa and pDG0100 differs from our sequences by one nucleotide. Two additional differences were an insert of 41 bases and a single base insertion between sulI and ORF341 in our sequence. Our sequenced regions have been assigned GenBank Accession Nos. UO4277 and UO4278 for the first and second sulI genes of pSa, respectively.

Cytochrome P450 CYP 2E1 induction during chronic alcohol exposure occurs by a two-step mechanism associated with blood alcohol concentrations in rats

Intragastric infusion of ethanol to male rats as part of a system of total enteral nutrition allows chronic ethanol treatment without the nutritional and feeding problems associated with traditional liquid diets. Even though ethanol was infused at a constant rate 24 h a day, blood alcohol concentrations were observed to cycle over a 5- to 7-day period from values less than 10 mg/dl to greater than 400 mg/dl. Examination of the hepatic microsomal mono-oxygenase system in animals chronically treated with ethanol using this model revealed variable induction of cytochrome P450 CYP 2E1, the principal component of the microsomal ethanol oxidizing system. Correlations were observed between urine alcohol concentrations (UACs) and 1) the level of expression of CYP 2E1 mRNA in Northern blot analysis, 2) the level of CYP 2E1 apoprotein in Western blot analysis and, 3) microsomal p-nitrophenol (PNP) hydroxylation. The data from ethanol-treated animals were expressed as low UAC group (UACs < 200 mg/dl) and a high UAC group (UACs > 300 mg/dl) and compared to total enteral nutrition controls. In the low UAC group, a 6- to 7-fold induction in microsomal PNP hydroxylase (a CYP 2E1-dependent activity) was accompanied by a 4- to 5-fold increase in CYP 2E1 apoprotein, but no increase in CYP 2E1 mRNA levels. In contrast, in the high UAC group, induction of PNP hydroxylase was 15- to 16-fold, induction of CYP 2E1 apoprotein was 12- to 13-fold and CYP 2E1 mRNA was elevated 5- to 6-fold.(ABSTRACT TRUNCATED AT 250 WORDS)

Effects of chronic ethanol on growth hormone secretion and hepatic cytochrome P450 isozymes of the rat

Growth hormone (GH) secretion is sexually dimorphic in the laboratory rat and the plasma GH profile is a determining factor in the regulation of the male-specific cytochrome P450 (CYP) 2C11. Acute ethanol has been reported previously to alter the secretion of GH, and in the present investigation, we have studied the effects of chronic (38 days) ethanol on plasma GH profiles, CYP 2C11 and the major ethanol-inducible cytochrome, CYP 2E1, using a total enteral nutrition system, where 35% of the total calories were ethanol. Ethanol-treated rats had elevated (P < or = .05) CYP 2E1 activities and apoprotein levels and increased steady-state mRNA levels encoding for CYP 2E1. Ethanol-treated rats also had reduced (P < or = .05) hydroxylation of testosterone at positions 2 alpha and 16 alpha, lower 2C11 apoprotein levels and lower steady-state mRNA levels encoding for 2C11. In addition, the plasma GH pulse profiles were altered in chronically treated rats by reducing (P < or = .05) the GH pulse amplitude and mean plasma GH concentrations. Our results suggest that: 1) the reduced CYP 2C11 activities, apoprotein levels and steady-state mRNA levels during chronic alcohol exposure are causally related to the alterations in GH secretion; and 2) chronic alcohol exposure elevated CYP 2E1 activities, apoprotein levels and steady-state mRNA levels, and these changes occurred primarily as the result of ethanol rather than undernutrition or as the combination of ethanol and undernutrition.

A correlation with type of sulfonamide resistance gene in Escherichia coli and synergy between trimethoprim and sulfamethoxazole

Plasmids carrying type I or II sulfonamide-resistance (Sur) genes were evaluated for their effect on synergy between trimethoprim (Tmp) and sulfamethoxyzole (Smx) in E. coli. Strain J53 containing each of three plasmids (R1, pSa, and R388) with the type I Sur gene displayed a synergistic response to Tmp/Smx; strain LE392 containing a plasmid (RSF1010) with the type II Sur gene displayed no synergy. The difference in synergy between type I and type II Sur genes might be explained by the difference in amount of resistant enzyme produced.

Evaluation of the variety of plasmid profiles in S epidermidis isolates from hospital patients and staff

Plasmid profiling was used to determine the variability of normal flora isolates of Staphylococcus epidermidis in order to evaluate the usefulness of plasmid profiling for identifying pathogens. Fifteen hospital staff members and patients repeatedly had cultures taken from the hands and nares, and multiple isolates were examined for plasmid profiles. S epidermidis isolated from the nares of 15 neonates were also examined. The total number of isolates examined for plasmid profiles was 726. Repetition of profiles was common among the different isolates from a single sampling (one swab). The frequency of re-isolating similar profiles on different days varied from 7% to 13%. Simultaneous isolation of similar profiles from nares and hands on the same individual varied from 0% to 11%, the percentage being lower for personnel. Isolation of the same plasmid profile from different individuals occurred only twice and resulted in an assignment probability of Pa = 0.002 for isolates obtained from different individuals. Significantly more isolates from nares contained plasmids (97%) compared with isolates from hands (89%). Patients who had two or more isolates of coagulase-negative staphylococci with similar profiles were judged, clinically, to have infections in 12 of 13 cases. However, the likelihood of re-isolating an S epidermidis strain with a similar plasmid profile twice from the same person at different times was sufficiently high to prevent plasmid profiling from being used as an absolute criterion for infection.

Restriction enzyme map of cryptic plasmid accompanying pR711b and pR409; identity of pR409 and pR388

A reference strain containing the IncW plasmid, pR409, was found to contain also a cryptic, conjugative plasmid, here named pJR15. After the separation of the two plasmids into different strains of bacteria, pR409 was found to have an identical restriction enzyme map to the IncW plasmid, pR388. Both pR409 and pR388 were isolated from the same hospital in London and confer sulphonamide and trimethoprim resistance. Originally pR409 was reported to confer resistance to tetracycline, but this was not confirmed by the Plasmid Reference Center. pR409 appears to represent another isolate of pR388 in a different host background. The restriction enzyme map of the cryptic plasmid, pJR15 (39 kb), has been determined. pJR15 was found compatible with plasmids from 15 different incompatibility groups and has been found also in the reference strain of the IncD plasmid, pR711b. The HindIII and BglII digests of pR711b are shown. The possible presence of the conjugative plasmid, pJR15, should be examined for studies on the sex pili or chromosomal mobilization properties of pR711b.

One-kilobase direct repeats of plasmid pSa

One-kilobase, direct repeats were found on either side of the chloramphenicol resistance gene of plasmid pSa. The right repeat corresponded to the region coding for sulfanilamide resistance. The repeats were not identical as judged by distances between restriction enzyme sites, hybridization, and by the ability to confer resistance to sulfanilamide.