Neal F. Cariello

Databases and software for the analysis of mutations in the human p53 gene, human hprt gene and both the lacI and lacZ gene in transgenic rodents

We have created databases and software applications for the analysis of DNA mutations at the humanp53gene, the humanhprtgene and both the rodent transgeniclacIandlacZlocus. The databases themselves are stand-alone dBASE files and the software for analysis of the databases runs on IBM-compatible computers. Each database has a separate software analysis program. The software created for these databases permit the filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web (WWW). Open the following home page with a Web Browser: http://sunsite.unc.edu/dnam/mainpage.ht ml . Alternatively, the databases and programs are available via public FTP from: anonymous@sunsite.unc.edu . There is no password required to enter the system. The databases and software are found beneath the subdirectory: pub/academic/biology/dna-mutations. Two other programs are available at the site-a program for comparison of mutational spectra and a program for entry of mutational data into a relational database.

Software for the analysis of mutations at the human hprt gene

Mutations at the human hypoxanthine-guanine phosphoribosyl transferase gene (hprt) are currently of great interest because mutations at this locus are being used as a biomonitor of human mutagenic exposure. Not only can somatic hprt mutants arising in vivo in humans be recovered and sequenced, but there is also a considerable body of information about the in vitro mutational spectra of different carcinogens at this locus. Previously, we reported the creation of a computerized database containing DNA-sequence information on human hprt mutants (Cariello et al. (1992) Environ. Mol. Mutagen., 20, 81-83). In the present manuscript, software for the analysis of mutations in the hprt database is described. Numerous routines have been developed for the analysis of single-base substitutions, including programs to (i) determine if two mutational spectra are different, (ii) display the number of mutations and mutable sites in each exon, (iii) determine if mutations show a DNA-strand bias, (iv) determine the frequency of transitions and transversions, (v) display the number and kind of mutations observed at each base in the coding region, (vi) perform nearest-neighbor analysis and (vii) display mutable amino acids in the hprt protein. The software runs only on IBM-compatible machines with MS-DOS. The software and hprt database is freely available via the INTERNET using remote file-transfer protocol. These programs simplify the analysis of the rapidly increasing information about hprt mutation. The programs permit the facile comparison between in vitro and in vivo data, as well as the identification of mutational patterns that may be of importance to experimenters using hprt as a biomonitor and and of importance to researchers studying mechanisms of mutation.

Deletion mutagenesis during polymerase chain reaction: dependence on DNA polymerase

Polymerase chain reaction (PCR) was performed with two polymerases. Thermus aquaticus DNA polymerase (Taq), and modified T7 DNA polymerase (Sequenase). Both polymerases were used to amplify the same portion of the human 18S rRNA gene. We report a PCR artifact, namely a deletion of 54 bp, when Taq polymerase was used to amplify a portion of the human 18S rRNA gene. PCR performed with Sequenase did not produce this artifact. The deletion eliminated a potentially stable hairpin loop. Our data are consistent with the following model for generation of the deletion: (i) the formation of an intrastrand hairpin, and (ii) polymerization across the base of the hairpin, thus deleting the nucleotide sequence in the hairpin. Furthermore, we show that the deletion occurs mainly during synthesis of the (-)DNA strand. Our observations suggest that similar artifacts may occur in other sequences containing stable secondary structures.

Responses of brown adipose tissue to diet-induced obesity, exercise, dietary restriction and ephedrine treatment

Drug-induced weight loss in humans has been associated with undesirable side effects not present in weight loss from lifestyle interventions (caloric restriction or exercise). To investigate the mechanistic differences of weight loss by drug-induced and lifestyle interventions, we examined the gene expression (mRNA) in brown adipose tissue (BAT) and conducted histopathologic assessments in diet-induced obese (DIO) mice given ephedrine (18 mg/kg/day orally), treadmill exercise (10 m/min, 1-h/day), and dietary restriction (DR: 26% dietary restriction) for 7 days. Exercise and DR mice lost more body weight than controls and both ephedrine and exercise reduced percent body fat. All treatments reduced BAT and liver lipid accumulation (i.e., cytoplasmic lipids in brown adipocytes and hepatocytes) and increased oxygen consumption (VO2 ml/kg/h) compared with controls. Mitochondrial biogenesis/function-related genes (TFAM, NRF1 and GABPA) were up-regulated in the BAT of all groups. UCP-1 was up-regulated in exercise and ephedrine groups, whereas MFSD2A was up-regulated in ephedrine and DR groups. PGC-1α up-regulation was observed in exercise and DR groups but not in ephedrine group. In all experimental groups, except for ephedrine, fatty acid transport and metabolism genes were up-regulated, but the magnitude of change was higher in the DR group. PRKAA1 was up-regulated in all groups but not significantly in the ephedrine group. ADRß3 was slightly up-regulated in the DR group only, whereas ESRRA remained unchanged in all groups. Although our data suggest a common pathway of BAT activation elicited by ephedrine treatment, exercise or DR, mRNA changes were indicative of additional nutrient-sensing pathways in exercise and DR.

Mixture deconvolution and analysis of Ames mutagenicity data

Abstract Mixtures abound in chemistry: two or more compounds may be present in the same sample, the same biological effect may be produced by two different mechanisms, or two compounds might bind to a receptor in different orientations or even in different places. Sometimes, results are given in summary form. For example, a chemical may be declared a mutagen due to any of several assay results from an Ames test. Clearly, a single mathematical model is not going to hold for data sets where such multiplicity of phenomena are represented. We need molecular descriptors and statistical methods which enable us to deconvolute such mixtures. Our idea is to combine topological chemical descriptors—augmented atoms and through-bond distance measures—with a statistical technique, segmentation recursive partitioning, that is capable of dealing with mixtures. The benefit is the ability to develop structure–activity relationships for large, heterogeneous data sets. We successfully demonstrate the effectiveness of the above descriptors and the technique of recursive partitioning with Ames test results taken from public sources.

Mutational analysis using denaturing gradient gel electrophoresis and PCR

Denaturing gradient gel electrophoresis (DGGE) separates (DNA) molecules based on their sequence. Using the proper conditions, all base-pair substitutions can be resolved from the wild-type sequence using DGGE. Polymerase chain reaction (PCR) permits rapid amplification of a given region of the genome. In this paper, we demonstrate the utility of DGGE combined with PCR for mutation analysis by presenting different examples: (i) analysis of mouse p53 cDNA for mutations, (ii) simultaneous analysis of thousands of 4NQO-induced mutants for mutations in HPRT exon 3, (iii) examination of the fidelity of the thermostable DNA polymerase isolated from Pyrococcus furiosus (Pfu), (iv) purification of mutant DNA from contaminating wild-type DNA from mouse spleenic T-cell clones.

In vivo mutation at the human HPRT locus

The molecular nature of mutations that arise in vivo at the human hypoxanthine-guanine phosphoribosyltransferase (HPRT) locus can be determined. A wide variety of such mutations can be detected, including large and small deletions, frameshift mutations and single-base substitutions, as well as alterations that cause aberrant mRNA splicing. Here, we review the available information on mutations at this locus.

A novel bacterial reversion and forward mutation assay based on green fluorescent protein

We report the first use of green fluorescent protein (GFP) for mutation detection. We have constructed a plasmid-based bacterial system whereby mutated cells fluoresce and non-mutated cells do not fluoresce. Fluorescence is monitored using a simple hand-help UV lamp; no additional cofactors or manipulations are necessary. To develop a reversion system, we introduced a +1 DNA frameshift mutation in the coding region of GFP and the resulting protein is not fluorescent in Escherichia coli. Treatment of bacteria containing the +1 frameshift vector with ICR-191 yields fluorescent colonies, indicating that reversion to the wild-type sequence has occurred. Site-directed mutagenesis was used to insert an additional cytosine into a native CCC sequence in the coding region of GFP in plasmid pBAD-GFPuv, expanding the sequence to CCCC. A dose-related increase in fluorescent colonies was observed when the bacteria were treated with ICR-191, an agent that induces primarily frameshift mutations. The highest dose of ICR-191 tested, 16 microg/ml, produced a mutant fraction of 16 x 10(-5) and 8.8 x 10(-5) in duplicate experiments. The reversion system did not respond to MNNG, an agent that produces mainly single-base substitutions. To develop a forward system, we used GFP under the control of the arabinose PBAD promoter; in the absence of arabinose, GFP expression is repressed and no fluorescent colonies are observed. When cells were treated with MNNG or ENNG, a dose-dependent increase in fluorescent colonies was observed, indicating that mutations had occurred in the arabinose control region that de-repressed the promoter. Treating bacteria with 100 microg/ml MNNG induced mutant fractions as high as 82 x 10(-5) and 40 x 10-5 in duplicate experiments. Treating bacteria with 150 microg/ml ENNG induced a mutant fraction of 2.1 x 10(-5) in a single experiment.

An Initial Characterization of N-Terminal-Proatrial Natriuretic Peptide in Serum of Sprague Dawley Rats

In the clinical setting, natriuretic peptides (NPs) have proven to be reliable noninvasive markers for diagnostic, prognostic, and therapeutic monitoring of heart failure. Given their proven utility in humans, NPs are potential candidates for translational biomarkers during drug development to detect drug-induced hemodynamic stress resulting in cardiac hypertrophy in preclinical species. We evaluated the intra- and interassay precision and the stability of serum N-terminal-proatrial natriuretic peptide (NT-proANP) using a commercially available enzyme-linked immunoassay (EIA). We then measured NT-proANP concentrations in 532 serum samples from 337 male Crl:CD(SD) rats with or without pressure-induced cardiac hypertrophy. Additionally, we established a reference range using samples from control animals across multiple studies. The data demonstrate that the NT-proANP EIA is a robust and reproducible assay for the measurement of NT-proANP. The noninvasive translational utility, minimal sample volume requirement, and the lack of existing hypertrophic biomarkers in the male rat make NT-proANP an excellent candidate for further interrogation as a biomarker of cardiac hypertrophy in preclinical toxicology investigations.

Database and software for the analysis of mutations at the lacI gene in both transgenic rodents and bacteria.

The use of transgenic rodents for the study of genetic toxicology has increased dramatically in the past several years. A great deal of the recent work has employed the lacl locus in transgenic mice. In addition to the transgenic data, a substantial amount of information exists regarding mutation of the lacl gene in bacteria. In an effort to centralize the information regarding mutations in the lacl gene in both rodents and bacteria, we have created a computerized database that contains information about DNA sequence alterations on about 500 mutations in transgenic rodents and 8,000 mutations in bacteria. We have also produced a software package for the analysis of the lacl database. Routines have been developed for the analysis of single base substitutions, including programs to (i) determine if two mutational spectra are different; (ii) determine if mutations show a DNA strand bias; (iii) determine the frequency of transitions and transversions; (iv) display the number and kind of mutations observed at each base in the coding region; (v) perform nearest neighbor analysis; and (vi) display mutable amino acids in the lacl protein. The software runs only on IBM‐compatible machines running Microsoft Windows. The software and lacl database are freely available via the Internet (http://sunsite.unc.edu/dnam/mainpage.html)