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J G de Boer

Publications and source records attributed to J G de Boer.

At least 19 recordsLinked to original sources
PubMed1997

The recovery of a B2 insertion in the lacI gene of a rat cell line containing a lambda/LIZ shuttle vector.

The bacterial lacI gene is in use as a reporter gene for mutation in transgenic mice, rats and in cell lines. During a mutagenesis study in which we used such a rat cell line, we recovered a mutant which features an insertion of a rat B2 repeated sequence element. This sequence element was inserted between positions 77 and 78 in the lacI gene. When the inserted sequence was compared to the published rat B2 sequences, two short deletions, possibly mediated by short repeat sequences, were revealed. This is the first demonstration of the recovery of a repeated sequence element into the lacI gene used in transgenic animals and cell lines, and confirms previous findings that such sequences indeed move around the genome.

Animals↗
PubMed1997

Spectrum of spontaneous mutations in liver tissue of lacI transgenic mice.

The advent of transgenic technology has greatly facilitated the study of mutation in animals in vivo. The Big Blue mouse system, transgenic for the lacI gene, permits not only the quantification of mutations in different tissues but also provides for the generation of in vivo-derived mutational spectra. This report details the sequence alterations of 348 spontaneous mutations recovered from the liver of 6-8-week-old male Big Blue mice. The spectra recovered from two strains of mice, C57BI/6 and B6C3F1, were compared and found to be very similar. The predominant mutations are G:C-->A:T transitions, with 75% of these occurring at 5'-CpG-3' sequences. This mutational bias is consistent with deamination-directed mutation at methylated cytosine bases. The second most common class of mutations is G:C-->T:A transversions. A significant clonal expansion of mutants was found in several animals, and this was used to make an approximate correction of the mutant frequency such that the most conservative estimate of mutation frequency is presented. The establishment of this substantial database of spontaneous mutations in the liver of Big Blue mice is intended to serve as a reference against which mutations recovered after treatment can be compared.

Animals↗
PubMed1996

Spontaneous mutants recovered from liver and germ cell tissue of low copy number lacI transgenic rats.

The finding of a large discordance between animal species in their response to a carcinogenic challenge, has led to the realization that the useful extrapolation of animal test data to humans requires a better understanding of animal interspecies differences. With the development of transgenic shuttle vector based animal systems we are now able to study mutation of the same genetic target in both mice and rats. We have begun to analyze mutants recovered from rat lines carrying low copy numbers of the same lambda/lacI constructs carried by the Big Blue mouse. A large database on mutations in lacI transgenic mice is already available for comparison. The data indicate that the differences between the mutations recovered from rat liver and germ cell tissues are similar to those recovered from transgenic mice, but when compared with a large database of mutations available for mice, some site-to-site differences may exist. This study represents the first interspecies look into the molecular nature of mutations in the lacI transgenic rodents.

Animals↗
PubMed1996

The genetic analysis of lacI mutations in sectored plaques from Big Blue transgenic mice.

The Big Blue lacI transgenic rodent assay, which uses the lambda LIZ/lacI gene as the target for mutation, provides a convenient short-term assay for the study of mutation in vivo [Kohler et al. (1991): Proc Natl Acad Sci USA 88:7958-7962; Provost et al. (1993): Mutat Res 288:133-149). However, the interpretation of data from transgenic animal assays is sometimes complicated by mutants that appear as sectored mutant lambda plaques. These mutants can form a significant fraction of the mutant plaques [Hayward et al. (1995): Carcinogenesis 16:2429-2433]. Thus, in order to accurately determine in vivo mutant frequencies and mutational specificities, it is necessary to score sectored plaques and partition them from the rest of the data. In this study, the specificity of mutation in sectored plaques recovered from untreated and UVB-treated Big Blue mouse skin was analyzed and compared to mutations recovered from lambda LIZ/lacI grown on the Escherichia coli host. The mutational spectra of sectored plaques from untreated and UVB-treated mice were remarkably similar to each other and resembled those recovered from the lambda LIZ/lacI phage plated directly on E. coli. Both the sectored mutants and those recovered in lambda LIZ/lacI phage differed from the spectra of spontaneous mutants in E. coli and in Big Blue mouse skin. While sectored mutants from UVB-treated mouse skin and lambda LIZ/lacI mutants were also different from spontaneous mutants recovered from Big Blue liver, these was little difference between sectored mutants from untreated mouse skin and spontaneous liver mutants (P = 0.07). The mutational spectra of sectored plaques is thus largely consistent with their origin as spontaneous mutations arising in vitro during growth of the lambda LIZ/lacI shuttle vector DNA on the E. coli host, although the potential contribution from lesions in mouse DNA being expressed ex vivo in the E. coli host cannot be excluded.

Animals↗
PubMed1996

An efficient laboratory protocol for the sequencing of large numbers of lacI mutants recovered from Big Blue transgenic animals.

Mutational spectra provide a powerful approach to investigate both the mutagenic potential and the mechanism of action of suspected mutagens and carcinogens. Recently, transgenic techniques have made it possible to generate mutational spectra in animals. Such a spectrum may consist of 50 to 200 mutants depending on the nature of the mutations, and many spectra can be generated depending on the design of the experiment. This report describes a practical approach for the processing and sequencing of large numbers of lacI mutants recovered from Big Blue animals.

Animals↗
PubMed1996

Spectrum of mutations in kidney, stomach, and liver from lacI transgenic mice recovered after treatment with tris(2,3-dibromopropyl)phosphate.

The flame retardant tris(2,3-dibromopropyl)phosphate (TDBP), once used in cotton sleep wear for children, is presently banned from commerce. It produces tumors in rodents in both a sex- and tissue-specific manner. The kidney is the main target for tumor formation in male and female rats, as well as in male mice. In contrast, tumors are formed in the liver of female animals. We have used lacI transgenic male B6C3F1 mice (Big Blue) to examine the induction of mutation in kidney, liver, and stomach after exposure to 150 mg/kg (2 days), 300 mg/kg (4 days), and 600 mg/kg (4 days) of TDBP. At the highest dose, the mutant frequency was approximately 50% above control values in the kidney (P < 0.01). A smaller increase was observed in the liver (P = 0.07), while no increase was seen in the stomach (P = 0.28). Sequence analysis of the recovered mutants showed a TDBP-specific change in mutation spectrum in kidney, which was not observed in liver and stomach. In kidney, a dose-dependent decrease in G:C-->A:T transitions, including at 5'-CpG-3' sites, was observed. This was accompanied by an increase in the loss of single G:C base pairs from approximately 3% to 15%. These results illustrate both the sensitivity and specificity of the lacI transgenic system in the analysis of tissue-specific mutation. This study also reinforces the importance of examining mutational spectra when mutant induction levels are low.

Animals↗
PubMed1996

Species-specific differences in hepatic mutant frequency and mutational spectrum among lambda/lacI transgenic rats and mice following exposure to aflatoxin B1.

In vivo mutations were studied in lambda/lacI (Big Blue) transgenic C57BL/6 mice and F344 rats following exposure to either AFB1 (aflatoxin B1) or DMSO vehicle. Fourteen days after exposure, livers were removed for DNA extraction and subsequent mutational analysis of the lacI gene. Mice injected with a single i.p. dose of AFB1 at 2.5 mg/kg did not show a significant increase in liver mutant frequency relative to vehicle-treated controls. DNA sequence analysis of lacI mutations collected from the AFB1-treated mice showed a pattern of mutation similar to that of the previously observed spontaneous mouse liver mutational spectrum. In contrast, rats subjected to one-tenth the mouse AFB1 dosage responded with an approximate 20-fold induction in liver mutant frequency over background. Sequencing of lacI mutations also revealed spectral differences between vehicle- and AFB1-treated rats. A large increase in G:C-->T:A transversions was observed among lacI mutations isolated from the AFB1-treated rats. This work is among the first multi-species in vivo mutagenicity studies using transgenic rodents harboring the same shuttle vector. Such multi-species in vivo assays may prove to be valuable in the areas of mechanistic analysis and risk assessment.

Aflatoxin B1↗
PubMed1995

Software package for the management of sequencing projects using lacI transgenic animals.

The bacterial lacI gene has been used for many years as a mutational target for the study of the mechanisms of mutation. A wealth of information has been collected for many mutagenic treatments and in strains with diverse DNA repair backgrounds. Recently this gene has been used in the construction of a transgenic mouse, named Big Blue, and a transgenic rat, as well as a rat cell line. The lacI gene in these animals and cells can conveniently be recovered and analyzed in bacteria. This makes it possible to study mutagenic potential of chemical compounds in vivo using a mammal. Tissue, strain, and gender specificity can be addressed. In addition, mutations recovered from tumour tissues or from animals with specific genetic backgrounds can be analyzed conveniently. The mammalian systems can produce large numbers of mutants that require computer assistance to manage the samples and the resulting DNA sequence data. Accordingly, a computer software system was developed. The system maintains an inventory of bacteriophage lambda lacI mutants and allows entry of mutant sequences while performing accuracy checks on the data. The software features several options for displaying lists of mutants. The system can perform several analyses, including mutant class compilations, mutational spectra comparisons, and clonal expansions analysis. An extensive database obtained from the bacterial lacI system is included with the software and can be analyzed along with mutants derived from transgenic animals.

Algorithms↗
PubMed1993

A fast and simple method to determine the clonal relationship among human T-cell lymphocytes.

For the analysis of mutation in human T-cell lymphocytes, it is crucial to determine the clonal relationship between isolated mutants, particularly if they harbour identical mutations. Here we report an efficient method to determine the clonal relationships between these cells. The method is based on the analysis of restriction fragment length polymorphisms of a polymerase chain reaction amplified, rearranged T-cell receptor gamma-gene. As few as 600 cells are sufficient, regular agarose gels can be used for the separation of the restriction fragments, no radioactive label is required, and results can be obtained in 2 days.

Base Sequence↗
PubMed1992

Mutations recovered in the Chinese hamster aprt gene after exposure to carboplatin: a comparison with cisplatin.

Platinum-based compounds such as cisplatin and carboplatin are currently used for the treatment of a variety of solid tumors. Their primary mode of action involves the production of cross-links in DNA. These compounds induce mutations in bacterial as well as in mammalian cells. Previously we determined the sequence specificity and mutational outcome in the Chinese hamster aprt gene in mutants isolated after exposure to cisplatin. The second-generation platinum drug, carboplatin, is of clinical relevance because it displays different and less toxic effects. Here we report the mutagenic specificity of this related compound. Mutations recovered after exposure to carboplatin display the same preference for sequences that contain 5'-AGG-3', 5'-AGA-3' and 5'-GAG-3' as was found for cisplatin. We thus conclude that the mutagenic outcome of exposure to carboplatin and cisplatin respectively, is similar, if not identical.

Adenine Phosphoribosyltransferase↗
PubMed1991

Mutational analysis of the structure and function of the adenine phosphoribosyltransferase enzyme of Chinese hamster.

We have analyzed the adenine phosphoribosyltransferase (APRT) enzyme from Chinese hamster ovary cells through the study of mutants that are able to grow in the presence of the toxic adenine analogue 8-azaadenine. The distribution of the amino acid alterations was analyzed in terms of the binding regions for the purine and phosphoribosylpyrophosphate substrates and a comparison was made with mutants known in human APRT and human, mouse and hamster hypoxanthine-guanine phosphoribosyltransferase. A number of mutants were found to cluster in several regions of the amino acid sequence. Residual enzyme activity with adenine was determined and this was correlated with substrate binding regions. A model of the secondary structure features is proposed.

Adenine Phosphoribosyltransferase↗
PubMed1989

Mutational specificity studies of endogenous mammalian cell loci: methodological aspects.

We report here the details of a modified cloning method first described by Seed et al. (1983) for use in an extensive study of mutational specificity at the aprt locus of Chinese hamster ovary cells. The technology depends on homologous recombination between a suppressor probe plasmid and the desired insert in a genomic library constructed in a double amber mutant bacteriophage lambda vector. Recombinant phage form blue plaques on a non-suppressor, lacZ amber host. We have determined the sensitivity of the method. Homologous recombination frequency is in the order of 10(-3), 6-7 orders of magnitude above non-homologous events. Recombination efficiency is unaffected when the target phage is diluted 100,000-fold with parental vector. A background of plaques is observed along with the desired blue plaques. Although the color discrimination permits us to easily avoid these background plaques, we have characterized the frequency and the nature of these events.

Adenine Phosphoribosyltransferase↗
PubMed1989

Sequence specificity of mutation induced by the anti-tumor drug cisplatin in the CHO aprt gene.

Cis-diammine dichloroplatinum (cisplatin) is an effective anti-cancer drug which forms adducts with DNA, in both bacterial and mammalian cells. It is suspected of producing tumors as well. To determine the molecular nature of genetic alterations induced by cisplatin, we cloned and sequenced cisplatin-induced mutants in the adenine phosphoribosyltransferase (aprt) gene of Chinese hamster ovary (CHO) cells. Mutation by cisplatin appears to be targeted as the sites of mutation are consistent with the known binding specificity of cisplatin. Many mutations occur at or proximal to the sequence 5'-AGG-3' and 5'-GAG-3' and include transversions, transitions, frameshifts and short deletions and duplications. Several double changes were also observed. No major rearrangements were recovered in our collection. At several locations, a number of mutants were found to be clustered within a small target region, but unlike traditional hotspots, these represent diverse changes occurring in a localized region of a few base pairs.

Adenine Phosphoribosyltransferase↗
PubMed1988

Base substitutions, frameshifts, and small deletions constitute ionizing radiation-induced point mutations in mammalian cells.

The relative role of point mutations and large genomic rearrangements in ionizing radiation-induced mutagenesis has been an issue of long-standing interest. Recent studies using Southern blotting analysis permit the partitioning of ionizing radiation-induced mutagenesis in mammalian cells into detectable deletions and major genomic rearrangements and into point mutations. The molecular nature of these point mutations has been left unresolved; they may include base substitutions as well as small deletions, insertions, and frame-shifts below the level of resolution of Southern blotting analysis. In this investigation, we have characterized a collection of ionizing radiation-induced point mutations at the endogenous adenine phosphoribosyltransferase (aprt) locus of Chinese hamster ovary cells at the DNA sequence level. Base substitutions represented approximately equal to 2/3 of the point mutations analyzed. Although the collection of mutants is relatively small, every possible type of base substitution event has been recovered. These mutations are well distributed throughout the coding sequence with only one multiple occurrence. Small deletions represented the remainder of characterized mutants; no insertions have been observed. Sequence-directed mechanisms mediated by direct repeats could account for some of the observed deletions, while others appear to be directly attributable to radiation-induced strand breakage.

Adenine Phosphoribosyltransferase↗
PubMed1988

An in vitro assay for frameshift mutations: hotspots for deletions of 1 bp by Klenow-fragment polymerase share a consensus DNA sequence.

The fidelity of in vitro DNA synthesis catalyzed by the large fragment of DNA polymerase I was examined. The templates, specifically designed to detect shifts to the +1 or to the -1 reading frame, are composites of M13mp8 and bacteriophage T4 rIIB DNA and were designed to assist in the identification of the types of frameshifts that are the specific consequence of DNA polymerization errors. In vitro polymerization by the Klenow fragment produced only deletions, rather than the mixture of duplications and deletions characteristic of in vivo frameshifts. The most frequent frameshifts were deletions of 1 bp opposite a template purine base. Hotspots for these deletions occurred when the template purine immediately preceded the template sequence TT. The highest mutation frequencies were seen when the TTPu consensus sequence was adjacent to G:C rich sequences in the 3' direction. The nature of the consensus sequence itself distinguishes this 1-bp deletion mechanism from those operating in DNA repeats and attributed to the misalignment of DNA primers during synthesis. Deletions that were larger than 1 or 2 bp isolated after in vitro replication were consistent with the misalignment of the primer. Deletions of 2 bp and complex frameshifts (the replacement of AA by C) were also found. Mechanisms that may account for these mutations are discussed.

Base Sequence↗
PubMed1984

Demonstration of the production of frameshift and base-substitution mutations by quasipalindromic DNA sequences.

The in vivo production of frameshift and base-substitution mutations predicted as a consequence of the metabolic processing of misaligned quasipalindromic DNA sequences has been confirmed. Spontaneous frameshift mutations of the T4 rII gene that had been genetically mapped to quasipalindromic DNA sequences were sequenced. Some of the mutant sequences are exactly those predicted by a mutational model based on misaligned quasipalindromes. Furthermore, these sequences are distinct from those predicted by the classical frameshift model based on misaligned repeated sequences. The rII frameshift mutant sequences reported here result from the deletion of a specific base or bases that would remain looped out should the quasipalindromes assume a hairpin secondary structure. One hairpin predicted not only the deletion of two bases (a frameshift) but the concomitant production of nearby but noncontiguous base substitutions. The substitution of as many as three bases as well as the frameshift were predicted to arise as a consequence of a single mutational event in the palindrome. Two independent examples of the predicted deletion frameshift were found among the small sample of sequenced spontaneous frameshifts examined and both were associated with the predicted transversion and transition base substitutions.

Base Sequence↗