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E Mullaart

Publications and source records attributed to E Mullaart.

At least 19 recordsLinked to original sources
PubMed1997

Mapping of 34 minisatellite loci resolved by two-dimensional DNA typing.

Two-dimensional (2-D) DNA typing is based on electrophoretic separation of genomic DNA fragments in two dimensions according to independent criteria (size and base-pair sequence), followed by hybridization analysis using multilocus probes. The technique allows simultaneous visualization of several hundred loci as spots in a 2-D pattern. The majority of the loci resolved are polymorphic. Using linkage analysis in a large CEPH family, this study reports the mapping of 34 loci detected by the minisatellite core probe 33.6. By multipoint linkage analysis, regional chromosome positions of the 33.6 loci could be deduced, showing no evidence of clustering. In the analysis of spot patterns, use was made of a computerized image analysis system specifically designed for 2-D DNA typing. Since experimental variations between different separation patterns were automatically corrected for with this program, rapid and reliable scorings could be obtained. The results presented demonstrate the availability of reliable genetic information throughout the 2-D separation pattern. Adding the use of semiautomated computerized pattern analysis, this study further substantiates the applicability of 2-D DNA typing in genome scanning, not only in theoretical but also in practical terms. Moreover, it can be anticipated that this method will have a specific advantage in studies that scan for trinucleotide repeat expansions and somatic instability, where the repeat sequences detected by appropriate core probes are of particular interest.

Chromosome Mapping↗
PubMed1996

Comprehensive and accurate mutation scanning of the CFTR gene by two-dimensional DNA electrophoresis.

The large number of possible disease-causing mutations in the 27 exons of the cystic fibrosis transmembrane conductance regulator (CFTR) gene has severely limited direct diagnosis of cystic fibrosis (CF) patients and carriers by mutation detection. Here we show that in principle testing for mutations in the CFTR gene can be both substantially facilitated and made virtually complete, by two-dimensional DNA electrophoretic separation of polymerase chain reaction (PCR) amplified exons on the basis of size and basepair sequence in denaturing gradient gels. Under a single optimized set of conditions we were able to obtain a pattern of spots representing all 27 exons of the CFTR gene and to readily detect 17 out of 17 identified sequence variations in 9 different exons in DNA from 11 CF patients and carriers. Our results demonstrate the potential of 2-dimensional DNA electrophoresis for comprehensive mutation analysis of the CFTR gene. The approach serves as a model for comprehensive diagnosis of the many other large disease genes for which a variety of mutations have also which been reported.

Cystic Fibrosis↗
PubMed1995

Two-dimensional DNA typing of human pedigrees: spot pattern characterization and segregation.

By two-dimensional (2-D) genome typing, i.e., electrophoretic separation of restriction enzyme-digested genomic DNA on the basis of both size and sequence in denaturing gradient gels followed by hybridization analysis, several hundred alleles (spots) can be analyzed in parallel, using a micro- or minisatellite core probe. We studied the segregation of 213 and 214 spots detected by microsatellite core probe (CAC)n and minisatellite core probe 33.6, respectively, in two three-generation human pedigrees. Reproducibility of the spot patterns was such that particular spot variants could be scored in both pedigrees. Between 73 and 74% of the spots scored were variant and were transmitted in a Mendelian manner. Very little cosegregation among the 2-D spots themselves was observed, suggesting a random distribution over the genome. Several pairs of spots that appeared to contain both alleles from single loci were identified. The few spots detected by both probes (overlapping spots) showed different segregation patterns, indicating that each probe detects independent sets of genetically informative loci. These results provide a firm basis for using 2-D DNA typing to identify disease loci and for constructing a 2-D spot genetic linkage map of the human genome.

Alleles↗
PubMed1995

Two-dimensional DNA typing as a genetic marker system in humans.

By two-dimensional (2-D) DNA typing several hundred genomic loci can be analysed simultaneously in a two-dimensional pattern as spots detected by micro- or minisatellite core probes. Many of these loci display DNA sequence polymorphisms, and we have examined whether it is possible to extract genetic information from the rather complex but potentially very informative 2-D DNA typing patterns. To do so, the segregation of 9 spots detected by the microsatellite core probe (CAC)n was followed in a large CEPH pedigree, and by linkage analysis it was possible to obtain chromosomal assignments of the corresponding (CAC)n loci in all cases except one. Furthermore, a regional, physical localization of these loci emerged from analysis of the existing genetic and physical localization data of DNA markers flanking the (CAC)n loci. We have hereby obtained evidence that the spots detected by the microsatellite core probe (CAC)n segregate in a Mendelian manner and that it is possible to reliably score the segregation of single spots within a family. These results indicate that the large amount of potential information inherent in 2-D DNA typing may be used as a genetic marker system; an important prerequisite for its application as a genome scanning method, e.g. in detection of genomic alterations in cancer and in mapping of genetic traits.

Chromosome Mapping↗
PubMed1994

Two-dimensional DNA electrophoresis in mutation detection.

Accurate detection of gene mutations is important in many areas of biology and medicine. In fundamental studies of mutagenesis it is often necessary to assess all possible mutations, either spontaneous or induced by genotoxic agents, in a particular gene or gene sequence to explain a given cellular or physiological endpoint. In molecular medicine comprehensive detection of all possible mutations in a disease gene is required before clinical genetic testing becomes feasible. Of the many mutation detection methods currently available none is capable of scanning for all possible mutations in a cost-effective manner. Here we show that by two-dimensional DNA electrophoretic separation, on the basis of both size and base pair sequence, in principle all mutations in a given gene can be detected. This is illustrated by some data on 2-D electrophoresis of 10 exons of the cystic fibrosis gene.

Cystic Fibrosis↗
PubMed1994

Genome scanning of breast cancers by two-dimensional DNA typing.

We have recently used two-dimensional DNA typing to detect genetic alterations in breast tumours. This method, which is based on size separation in neutral gels and sequence separation in denaturing gradient gels followed by hybridisation analysis with mini- and microsatellite core probes, allows the simultaneous analysis of hundreds of allelic fragments in a very short time. Here we demonstrate the potency of this method for total genome scanning of the tumour genome by analysing a small series of breast cancers. Comparison of tumour and normal DNA from ten breast cancer patients, using two-dimensional DNA typing with four core probes, revealed a considerable number of genomic alterations. In contrast, with Southern blot analysis only a few alterations were observed using the same probes. Most of the changes observed (74%) were deletions (absence of spots in the tumour) while 20% corresponded to amplifications (spots of higher intensity in the tumour) and 5% were new spots (gains). About 10% of the genomic changes detected appeared to occur in the tumours of more than one patient.

Base Sequence↗
PubMed1993

Parallel genome analysis by two-dimensional DNA typing.

By two-dimensional (2-D) DNA typing a restriction enzyme digest of genomic DNA can be resolved on the basis of both size and base-pair sequence and subsequently analysed by repeat probe hybridization to reveal sequence variants at multiple genomic sites in parallel. The system has been partly automated and allows for large-scale comparative analysis of complex genomes in a cost-effective manner.

Automation↗
PubMed1993

Genome scanning of human breast carcinomas using micro- and minisatellite core probes.

We have analyzed tumor and lymphocyte DNA from six breast cancer patients by one- and two-dimensional DNA fingerprinting using micro- and minisatellite core probes to estimate the extent and nature of DNA alterations in tumors. Both approaches were compared regarding sensitivity in genome analysis. We find that the number of deletions and amplifications increases linearly with the number of restriction fragments analyzed using the two-dimensional approach, as compared with the number found using the more traditional one-dimensional method. A set of four micro- and minisatellite core probes resulted in a total number of approximately 70 bands per patient using one-dimensional analysis of RsaI-digested DNA. When the same DNA was analyzed with the two-dimensional approach about 300 analyzable spots were resolved. In one patient, the tumor DNA contained 11 amplified spots and 14 deleted spots when compared to the patients lymphocyte DNA. Using HaeIII-digested DNA, a maximum of 845 spots could be observed, with only three probes.

Adult↗
PubMed1993

Linkage analysis by two-dimensional DNA typing.

In two-dimensional (2-D) DNA typing, genomic DNA fragments are separated, first according to size by electrophoresis in a neutral polyacrylamide gel and second according to sequence by denaturing gradient gel electrophoresis, followed by hybridization analysis using micro- and minisatellite core probes. The 2-D DNA typing method generates a large amount of information on polymorphic loci per gel. Here we demonstrate the potential usefulness of 2-D DNA typing in an empirical linkage study on the red factor in cattle, and we show an example of the 2-D DNA typing analysis of a human pedigree. The power efficiency of 2-D DNA typing in general is compared with that of single-locus typing by simulation. The results indicate that, although 2-D DNA typing is very efficient in generating data on polymorphic loci, its power to detect linkage is lower than single-locus typing, because it is not obvious whether a spot represents the presence of one or two alleles. It is possible to compensate for this lower informativeness by increasing the sample size. Genome scanning by 2-D DNA typing has the potential to be more efficient than current genotyping methods in scoring polymorphic loci. Hence, it could become a method of choice in mapping genetic traits in humans and animals.

Alleles↗
PubMed1991

Induction and disappearance of DNA strand breaks in human peripheral blood lymphocytes and fibroblasts treated with methyl methanesulfonate.

The induction and disappearance of DNA single-strand breaks (SSB) in human peripheral blood lymphocytes (PBL) and fibroblasts exposed to methyl methanesulfonate (MMS) were investigated by using the alkaline filter elution assay. In the two cell types, identical amounts of SSB were induced during a 45-min treatment with a given dose of MMS. In quiescent PBL only 9 +/- 4% (mean +/- SD) of the induced SSB had disappeared at 1 h after exposure, whereas in phytohemagglutinin-stimulated PBL, 23 +/- 12% disappeared within the same repair period. The percentage SSB disappearance in confluent fibroblasts was 25 +/- 2% at 1 h after exposure. As in PBL, the percentage SSB disappearance in fibroblasts appeared to be proliferation-dependent; actively dividing fibroblasts removed 50 +/- 12% of the MMS-induced SSB during the 1-h repair period. The accumulation of SSB in PBL, but not in fibroblasts, during MMS exposure in the presence of the excision-repair inhibitor 1-beta-D-arabinofuranosylcytosine indicated the utilization of different repair pathways in these two cell types. The generally lower rate of disappearance of MMS-induced SSB in PBL as compared to fibroblasts correlated with an increased loss of cell viability, measured by determining the incorporation of [3H]thymidine.

Cell Division↗
PubMed1991

Induction and disappearance of DNA strand breaks and/or alkali-labile sites in human lymphocytes exposed to N-ethyl-N-nitrosourea.

We investigated the induction and disappearance of DNA lesions that are detected as single-strand breaks (SSBs) with the alkaline filter elution technique, in human peripheral blood lymphocytes (PBLs) following exposure to N-ethyl-N-nitrosourea (ENU). In PBLs of the 15 individuals studied, 35 +/- 16% (mean +/- SD) of the SSBs present at the end of a 20 min treatment disappeared within 1 h; up to 24 h post-treatment no further disappearance was observed. Interindividual differences in SSB disappearance were considerable; in two cases, almost no SSBs disappeared over the 1 h period. In PBLs of the same 15 individuals 85 +/- 3% (mean +/- SD) of the SSBs induced by 4 Gy of gamma-rays were found to disappear within 1 h, which indicated no interindividual differences. Multiple blood sampling at 1 month intervals indicated that interindividual differences in ENU-induced SSB repair are constant and do not vary with time. The low rate of SSB disappearance appeared to correlate with low cell survival after ENU exposure, measured as a reduction in phytohemagglutinin-stimulated incorporation of [3H]-thymidine. The cytosine analog 1-beta-D-arabinofuranosyl-cytosine completely inhibited SSB disappearance, indicating that the removal of the repairable ENU-induced SSBs involves excision repair events.

Cell Survival↗
PubMed1990

Spontaneous DNA breaks in the rat brain during development and aging.

The level of spontaneous DNA breaks in nuclei isolated from the cerebral cortex of rat embryos at 12, 15 and 19 days of gestation, and from cerebral cortex and cerebellum of 24-day-, 6-month- and 36-month-old rats was measured by alkaline elution. A constant low level of DNA breaks was found in brain DNA during development from an embryo at day 12 of gestation to a 24-day-old rat. During aging the level of DNA breaks remained at the same low level, as shown by comparing nuclei from the cerebral cortex and cerebellum of 6- and 36-month-old animals. By contrast, an almost 2-fold increase in the level of DNA breaks was observed in rat liver nuclei between 6 and 36 months of age, confirming our earlier findings on isolated liver cells. Although there were no changes in the level of DNA breaks in rat brain during development or during aging, breaks accumulated rapidly post mortem. The rate of this process was not age-dependent. Our data suggest that the level of spontaneous DNA breaks in the brain is not likely to be of fundamental importance in the complex cellular alterations associated with brain development and aging.

Aging↗
PubMed1989

Age-related induction and disappearance of carcinogen-DNA-adducts in livers of rats exposed to low levels of 2-acetylaminofluorene.

It was investigated whether in vivo aging of rat liver is associated with changes in the induction and rate of disappearance of DNA damage. For this purpose 6- and 36-month-old rats were intraperitoneally injected with a single, low dose (5 mg/kg body wt.) of the model liver carcinogen 2-acetylaminofluorene (AAF). Using the 32P-postlabeling assay we found that N-(deoxyguanosin-8-yl)-2-aminofluorene (dG-C8-AF) was the major DNA-adduct formed. The minor adduct N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (dG-C8-AAF) could only be detected after doses of 20 mg/kg or more. Quantitation of adduct levels at various time points after treatment indicated a rapid induction of AF-adducts, which were already present at 6 h after treatment. The subsequent loss of AF-adducts was relatively slow, as was indicated by the presence of a substantial amount of AF-adducts as late as 21 days after treatment. Slight age-related differences in the pattern of induction and disappearance of AF-adducts and a somewhat higher level of persisting lesions in old than in young rats were observed.

2-Acetylaminofluorene↗
PubMed1989

Quiescent human peripheral blood lymphocytes do not contain a sizable amount of preexistent DNA single-strand breaks.

Sedimentation of nucleoids through neutral sucrose density gradients has shown that nucleoids isolated from phytohemagglutinin (PHA)-stimulated human peripheral blood lymphocytes (PBL) sediment faster than nucleoids derived from quiescent lymphocytes, which was attributed to rejoining of DNA single-strand breaks (SSB) present in the resting cells (A.P. Johnstone, and G.T. Williams (1982) Nature (London) 300, 368). We isolated PBL from donors and determined the amount of SSB in nonradiolabeled, untreated resting and PHA-stimulated cells by applying the alkaline filter elution technique. Calibration was based on dose-dependent induction of SSB by 60Co-gamma-radiation. Quiescent cells did not contain a sizable amount of SSB. Mitogen-stimulated cells showed equally low amounts of SSB per cell. The present study indicates that the interpretation of the results obtained with the nucleoid sedimentation technique concerning the supposed rejoining of SSB in PHA-stimulated human lymphocytes is incorrect. Other, equally sensitive, techniques such as alkaline filter elution appear to be preferable for studies on DNA damage and repair.

DNA Damage↗
PubMed1989

Effects of lethal exposure to hyperoxia and to hydrogen peroxide on NAD(H) and ATP pools in Chinese hamster ovary cells.

Cell death by oxidative stress has been proposed to be based on suicidal NAD depletion, typically followed by ATP depletion, caused by the NAD-consuming enzyme poly(ADP)ribose polymerase, which becomes activated by the presence of excessive DNA-strand breaks. In this study NAD+, NADH and ATP levels as well as DNA-strand breaks (assayed by alkaline elution) were determined in Chinese hamster ovary (CHO) cells treated with either H2O2 or hyperoxia to a level of more than 80% clonogenic cell killing. With H2O2 extensive DNA damage and NAD depletion were observed, while at a higher H2O2 dosage ATP also became depleted. In agreement with results of others, the poly(ADP)ribose polymerase inhibitor 3-aminobenzamide completely prevented NAD depletion. However, both H2O2-induced ATP depletion and cell killing were unaffected by the inhibitor, suggesting that ATP depletion may be a more critical factor than NAD depletion in H2O2-induced killing of CHO cells. With hyperoxia, only moderate DNA damage (2 X background) and no NAD depletion were observed, whereas ATP became largely (70%) depleted. We conclude that (1) there is no direct relation between ATP and NAD depletion in CHO cells subjected to toxic doses of H2O2 or hyperoxia; (2) H2O2-induced NAD depletion is not by itself sufficient to kill CHO cells; (3) killing of CHO cells by hyperoxia is not due to NAD depletion, but may be due to depletion of ATP.

Adenosine Triphosphate↗
PubMed1989

The removal of UV-induced pyrimidine dimers from DNA of rat skin cells in vitro and in vivo in relation to aging.

Young and old rats were compared with respect to the capacity of their skin fibroblasts and epidermal keratinocytes to remove low levels of ultraviolet light (UV) induced UV-endonuclease sensitive sites (pyrimidime dimers) from their DNA, in vitro and in vivo, respectively. In vitro, over a 24-h time period, fibroblasts from both young and old rats were found to remove about 20% of the pyrimidine dimers originally induced by 4.6 J/m2 of UV-C. In vivo, after 2.6 kJ/m2 of UV-B hardly any UV lesions were found to be present in fibroblasts, as demonstrated by immunohistochemistry using an anti-thymine dimer antibody. As reported earlier (Mullaart et al., J. Invest. Dermatol., 90 (1988) 346-349) cultured epidermal keratinocytes do not differ from cultured fibroblasts in UV repair kinetics, whereas in vivo they remove at least 50% of the pyrimidine dimers induced by 4 kJ/m2 of UV-B within 3 h. We now show that epidermal keratinocytes from old rats are not deficient in their in vivo repair characteristics upon this low UV-B dose. However, since a considerable fraction of the pyrimidine dimers appeared to be persistent in fibroblasts and keratinocytes, demonstrated by both enzymatic and immunochemical assays, the possibility is discussed that long-term exposure of skin cells to UV may lead to an accumulation of DNA damage with age.

Aging↗