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PubMed1991

Isolation and characterization of DNA from archaeological bone.

DNA was extracted from human and animal bones recovered from archaeological sites and mitochondrial DNA sequences were amplified from the extracts using the polymerase chain reaction. Evidence is presented that the amplified sequences are authentic and do not represent contamination by extraneous DNA. The results show that significant amounts of genetic information can survive for long periods in bone, and have important implications for evolutionary genetics, anthropology and forensic science.

Animals↗

PubMed2000

Megaplex DNA typing can provide a strong indication of the authenticity of ancient DNA amplifications by clearly recognizing any possible type of modern contamination.

Recent experiments revealed the perfect applicability of megaplex typing by autosomal short tandem repeats (STRs) to degraded DNA. The advantages of megaplex approaches lie in reduced amounts of sample material that are necessary and in remarkable time saving. Furthermore, megaplex typing clearly recognizes possible contaminations and thus has a large potential for indicating authenticity in ancient DNA analysis. This is demonstrated by three examples in which various types of contaminations could clearly be identified as such and even traced back to their origin. This would have been impossible using control samples, due to the sporadic nature of these types of contaminations.

Artifacts↗

PubMed1990

S1-nuclease enhancement of the ethidium bromide binding assay of drug-induced DNA interstrand crosslinking in human brain tumor cells.

A modification, using S1-nuclease, of a simple and sensitive fluorometric assay with ethidium bromide was developed for the measurement of cellular DNA interstrand crosslinking induced by bifunctional alkylators. Cells are lysed and treated with proteinase K and sodium dodecyl sulfate followed by extensive dialysis to yield intact high-molecular-weight DNA, free of contaminating proteins, on which the crosslink assay is then performed. The assay depends on the differential binding of ethidium bromide to single- and double-stranded DNA. Because of the higher ethidium bromide binding capacity of double-stranded DNA, the fluorescence retained after a heating/cooling cycle is directly proportional to the drug-induced cellular DNA interstrand crosslinking. We demonstrate that the sensitivity of this assay can be increased up to fourfold by including an S1-nuclease digestion step. This modified technique is simple and suited to the quantitation of low levels of DNA-interstrand crosslinking in cells.

Alkylating Agents↗

PubMed2001

Effect of DNA concentration on transgenesis rates in mice and pigs.

A retrospective analysis of transgenesis rates obtained in seven pronuclear microinjection programs was undertaken to determine if a relationship existed between the amount of DNA injected and transgenesis rates in the pig. Logistic regression analysis showed that as the concentration of DNA injected increased from 1 to 10 ng/microl, the number of transgenics when expressed as a proportion of the number liveborn (integration rate) increased from 4% to an average of 26%. A similar relationship was found when the number of molecules of DNA injected per picolitre was analysed. No evidence was obtained to suggest either parameter influenced integration rate in mice when the same constructs were injected. The number of transgenics liveborn when expressed as a proportion of ova injected (efficiency rate), increased as DNA concentration increased up to 7.5 ng/microl and then decreased at 10 ng/microl for both species suggesting that at this concentration DNA (or possible contaminants) may have influenced embryo survival. The relationship between efficiency and the number of molecules injected per picolitre was complex suggesting that the concentration at which DNA was injected was a better determinant of integration and efficiency rates. In conclusion, the present study suggests that transgenes need to be injected at concentrations of between 5 and 10 ng/microl to maximise integration and efficiency rates in pigs.

Animals↗

PubMed1995

Perinatal infection and persistence of human papillomavirus types 16 and 18 in infants.

Perinatal transmission of genital human papillomaviruses (HPVs), including HPV-16 and -18 which are associated with anogenital carcinomas have been described previously [Pakarian et al. (1994): British Journal of Obstetrics and Gynaecology 101:514-517; Kaye et al. (1994) Journal of Medical Virology 44:415-421]. A study was undertaken to investigate whether HPV-16 and -18 DNA in infants contaminated at delivery persists until they are 6 months of age. Of 61 pregnant women recruited, 42 (68.8%) were HPV-16 and 13 (21.3%) were HPV-18 DNA positive. At 24 hr there were transmission rates from HPV DNA positive mothers to their infants of about 73% (HPV-16: 69%; HPV-18: 76.9%). Ten mothers who were both HPV-16 and -18 DNA positive produced six (60%) infants who were also doubly positive at 24 hr. HPV DNA persisted to 6 weeks in 79.5% (HPV-16: 84%; HPV-18: 75%) of those infants who were positive at birth. At 6 months of age, persistent HPV-16 DNA was detected in 83.3% of cases, but HPV-18 DNA persistence at this time was 20%. To extend these observations over a greater age range of children HPV-16 L1 and L2 proteins were expressed in insect cells via recombinant baculoviruses and sera from 229 children were examined to determine at what age IgM antibodies to HPV were acquired. There was a bimodal distribution of IgM seropositivity which peaked between 2 and 5 and 13 and 16 years of age, suggesting that two distinct modes of transmission may occur. The observation that infection with high cancer risk genital HPVs may occur in early life and persist is of considerable importance for HPV vaccine strategies.

Adolescent↗

PubMed2005

Potential limitations of the 16S-23S rRNA intergenic region for molecular detection of Bartonella species.

PCR targeting the 16S-23S rRNA gene intergenic transcribed spacer (ITS) region has been proposed as a rapid and reliable method for the detection of Bartonella species DNA in clinical samples. Because of variation in ITS sequences among Bartonella species, a single PCR amplification can be used to detect different species within this genus. Therefore, by targeting the ITS region, multiple PCRs or additional sample-processing steps beyond the primary amplification can be avoided when attempting to achieve molecular diagnostic detection of Bartonella species. Although PCR amplification targeting this region is considered highly sensitive, amplification specificity obviously depends on primer design. We report evidence of nonspecific PCR amplification of Mesorhizobium species with previously published primers that were designed to amplify the Bartonella consensus ITS region. Use of these or other, less species-specific, primers could lead to a false-positive diagnostic test result when evaluating clinical samples. We also report the presence of Mesorhizobium species DNA as a contaminant in molecular-grade water, a series of homologous sequences in the ITS region that are common to Bartonella and Mesorhizobium species, the amplification of Mesorhizobium DNA with unpublished primers designed in our laboratory targeting the ITS region, and the subsequent design of unambiguous ITS primers that avoid nonspecific amplification of Mesorhizobium species. Our results define some potential limitations associated with the molecular detection of Bartonella species in patient samples and indicate that primer specificity is of critical importance if the ITS region is used as a diagnostic target for detection of Bartonella species.

Bartonella↗

PubMed1981

Further characterization of isolated presumptive euchromatin fractions of mouse hepatoma cells utilizing a cDNA probe complementary to the homologous poly(A)+ mRNA.

Poly(A)+ mRNA from mouse hepatoma ascites cell cytoplasm is characterized by three frequency classes: an abundant frequency class of a limited number of different nucleotide sequences, a less abundant frequency class of a larger number of different nucleotide sequences, and a rare frequency class containing a high number of different nucleotide sequences. [3H]cDNA synthesized on this poly(A)+ mRNA template hybridizes with some of the DNAs of the putative transcribable euchromatin fraction at a significantly faster rate than with total DNA if residual contaminating RNA is not removed. Following NaOH incubation to remove such RNA, the cDNA probe hybridized with essentially the same rate to the euchromatin fractions and total DNA. Nick translation of the nuclease-sensitive sequences of chromatin demonstrated that, even with limited nuclease digestion, the excised sequences rapidly converted to small oligonucleotides. The nick-translatable, small chromatin segments showed no enrichment for transcribable sequences. Chromatin segments, which distribute to the 50S-70S glycerol gradient fractions and which satisfy several of the presumptive criteria for enrichment for transcribable sequences, therefore show no enrichment for sequences complementary to the cDNA for poly(A)+ mRNA.

Animals↗

PubMed1994

Comparison of DNA polymerases alpha, delta, and epsilon of mouse cell line FM3A and its temperature-sensitive mutant tsFT20.

DNA polymerases (pol) alpha, delta and epsilon of a mouse cell line FM3A and its temperature-sensitive derivative tsFT20, which is defective in DNA replication at a non-permissive temperature, were purified by chromatographic procedures monitored by a set of relatively specific assays for the respective DNA polymerase activities. The pol epsilon activity was separated into two fractions with similar enzymatic properties except for their optimal KCl concentrations and processivities. The fractions of pol delta and epsilon were not homogeneous, but their identities were confirmed by their sensitivities to DNA polymerase inhibitors, their associated 3'-->5' exonuclease activities, optimal concentrations of salts, dependencies on the proliferating cell nuclear antigen and processivities in polymerization, which also excluded significant contamination with other DNA polymerases. Of the DNA polymerases prepared from tsFT20 cells, only pol alpha showed greatly decreased activity and remarkable sensitivity to the non-permissive temperature, demonstrating that pol delta and epsilon, the other polymerases supposed to be involved in nuclear DNA replication, are unequivocally different entities from pol alpha. The level of pol epsilon activity tsFT20 was also significantly lower than in the parental cells, suggesting cooperation and/or interaction between pol alpha and epsilon, and some relevance of pol epsilon to DNA replication.

Animals↗

PubMed1991

Comparative study of a DNA hybridization method and two isolation procedures for detection of Yersinia enterocolitica O:3 in naturally contaminated pork products.

We compared a DNA-DNA hybridization assay, using a synthetically produced oligonucleotide probe, and two conventional isolation procedures (methods A and B) with regard to their relative efficiency in detecting Yersinia enterocolitica O:3 in naturally contaminated pork products. Method A was as described by Wauters et al. (Appl. Environ. Microbiol. 54:851-854, 1988). Method B has been recommended by the Nordic Committee on Food Analysis (method no. 117, 1987). The genetic probe was used in a colony hybridization assay to detect virulent yersiniae at each of the isolation steps with composed methods A and B. A total of 50 samples of raw pork products obtained from 13 meat-processing factories in Norway were examined. Y. enterocolitica serogroup O:3, biovar 4, was isolated from altogether 9 (18.0%) of the samples by using the two isolation procedures. In contrast, colony hybridization using the genetic probe indicated that 30 (60.0%) of the samples contained virulent yersiniae. All samples which were positive on cultivation were also positive by hybridization. The results indicate that the occurrence of pathogenic Y. enterocolitica in Norwegian pork products is substantially higher than previously demonstrated and, therefore, reinforce our suggestion that pork products represent an important potential source of human infection in Norway. The results also indicate that the use of conventional isolation procedures may lead to considerable underestimation of pathogenic Y. enterocolitica in pork products.

Animals↗

PubMed2001

Prenatal HLA typing of uncultured amniocytes prior to the collection of related allogeneic cord blood.

DNA samples isolated from corresponding uncultured amniotic fluid, cord blood and maternal blood (n=5) were subjected to low resolution typing of the HLA-A, -B and -DRB loci by the polymerase chain reaction using sequence-specific primers (PCR-SSP). Furthermore, the effect of ethylene diamine tetraacetate disodium salt (EDTA) on the quality of genomic DNA isolated from amniotic fluid samples after long-term storage was evaluated. Unambiguous results of HLA typing could be achieved from all amniotic fluid samples stabilized with EDTA. PCR-SSP typing failed in DNA samples from amniotic fluid without the addition of EDTA. In all cases the fetal HLA type could be confirmed by the result from the corresponding cord blood typing. Contamination with maternal DNA led to additional weak PCR-SSP bands in one case, but data interpretation was still unambiguous. Reliable fetal HLA typing can be achieved directly from amniotic fluid and culturing of amniocytes is not required.

Amniocentesis↗

PubMed2004

A whole-genome mouse BAC microarray with 1-Mb resolution for analysis of DNA copy number changes by array comparative genomic hybridization.

Microarray-based comparative genomic hybridization (CGH) has become a powerful method for the genome-wide detection of chromosomal imbalances. Although BAC microarrays have been used for mouse CGH studies, the resolving power of these analyses was limited because high-density whole-genome mouse BAC microarrays were not available. We therefore developed a mouse BAC microarray containing 2803 unique BAC clones from mouse genomic libraries at 1-Mb intervals. For the general amplification of BAC clone DNA prior to spotting, we designed a set of three novel degenerate oligonucleotide-primed (DOP) PCR primers that preferentially amplify mouse genomic sequences while minimizing unwanted amplification of contaminating Escherichia coli DNA. The resulting 3K mouse BAC microarrays reproducibly identified DNA copy number alterations in cell lines and primary tumors, such as single-copy deletions, regional amplifications, and aneuploidy.

Animals↗

PubMed1998

An unusual DNA adduct derived from the powerfully mutagenic environmental contaminant 3-nitrobenzanthrone.

The covalent binding of an N-hydroxy metabolite of the powerfully mutagenic 3-nitrobenzanthrone (NBA) to 2'-deoxyguanosine (dG) and calf thymus DNA has been investigated in vitro. The major adduct obtained from the reaction of the N-acetoxy-N-acetyl derivative (N-Aco-N-Ac-ABA) of 3-aminobenzanthrone (ABA) and dG was identified as N-acetyl-3-amino-2-(2'-deoxyguanosin-8-yl)benzanthrone (dG-N-Ac-ABA) by 1H NMR and mass spectroscopies as well as by the reaction of N-Aco-N-Ac-ABA with the double-stranded calf thymus DNA. The coupling with the dG moiety occurred exclusively at C-2 of benzanthrone (BA), suggesting a significant contribution of a resonance-stabilized arenium ion intermediate derived from BA to the production of this new type of adduct. The preferred conformation of the adduct has been shown to be syn by 1H and 13C NMR.

Animals↗

PubMed1991

Extraction of DNA from amniotic fluid cells for the early prenatal diagnosis of genetic disease.

Ten-ml samples of amniotic fluid were taken from pregnancies being terminated at 8-14 weeks' gestation. DNA was extracted from the amniotic cells by sequential centrifugation and analysed using the polymerase chain reaction (PCR). Fifteen samples were analysed for evidence of maternal contamination using Mfd5 oligonucleotide primers for repeat polymorphisms. Ten amniotic fluid samples were tested for the Delta-F508 deletion characteristic of cystic fibrosis to demonstrate a diagnostic application for the technique. In each case, DNA extracted from fetal tissue from the same pregnancy was included in the controls. In 14 of the 15 cases tested with the Mfd5 primers, both the amniotic fluid DNA and the fetal DNA showed no evidence of contaminating DNA. In one case, neither the amniotic fluid cells nor the fetal cells yielded results. In nine of the ten cases tested with the Delta-F508 primers, the amniotic fluid cell DNA provided accurate information about the genetic status of the fetus; in the tenth, the fetal DNA failed to amplify. The results indicate that adequate DNA can be extracted from amniotic fluid from 8 weeks' gestation onward and these samples are suitable for prenatal diagnosis using PCR.

Adult↗

PubMed2001

Comparative analysis of PAH:DNA adducts formed in lung of mice exposed to neat coal tar and soils contaminated with coal tar.

7H-Benzo[c]fluorene (benzo[c]fluorene) is a major DNA adduct forming component of coal tar in lung of mice. The present study evaluated the types of PAH:DNA adducts formed from different neat coal tar samples and soils contaminated with coal tar. Mice were fed diets containing coal tar either neat or as a contaminant in an environmental soil sample for 14 days, and the types of chemical:DNA adducts formed in lung were evaluated using 32P-postlabeling and HPLC analysis. Three major DNA adducts derived respectively from benzo[b]fluoranthene (B[b]F), benzo[a]pyrene (B[a]P), and benzo[c]fluorene were detected in three of the four neat coal tar samples evaluated. In contrast, only a single major DNA adduct derived from benzo[c]fluorene was observed with the remaining tar sample. Ingestion of coal tar contaminated soil resulted in DNA adducts primarily derived from benzo[c]fluorene and B[b]F; a B[a]P derived DNA adduct was not detected. The DNA adducts derived from benzo[c]fluorene and B[b]F but not B[a]P were also observed with animals fed methylene chloride extracts of three of these soils but not the one designated A1000H soil. However, the extract of A1000H resulted in a B[a]P:DNA adduct being detected along with adducts formed from B[b]F and benzo[c]fluorene. The selective formation of the benzo[c]fluorene:DNA adduct with coal tar contaminated soils indicates that the in vivo systemic bioavailability and/or metabolism of benzo[c]fluorene is relatively high when compared to other DNA adducting hydrocarbons within coal tar. Benzo[c]fluorene may play a critical role in the potential of contaminated soil to induce a toxicological response in animals.

Administration, Oral↗

PubMed1990

Overview of studies on liver carcinogenesis in English sole from Puget Sound; evidence for a xenobiotic chemical etiology. II: Biochemical studies.

The levels of aromatic hydrocarbons in sediments of Puget Sound, Washington, are positively correlated with the prevalence of hepatic neoplasms and related lesions in English sole (Parophrys vetulus). To investigate the biochemical processes involved in chemical carcinogenesis in fish from Puget Sound, we have studied the uptake, activation, and detoxication of polycyclic aromatic hydrocarbons (PAHs) in English sole, and have compared these data to PAH metabolism in a related species, starry flounder (Platichthys stellatus), which shows a lower prevalence of hepatic neoplasms than sole. The results of both laboratory and field studies show that sediment-associated PAHs are biologically available to both flatfish species, and that both species accumulate similar levels of PAHs. Analyses of hepatic DNA from sole using the 32P-postlabeling technique indicate that xenobiotic chemicals were adducted to hepatic DNA of fish from the contaminated sites but not to the DNA of fish from reference sites. Studies of the ability of English sole and starry flounder to metabolize benzo(a)pyrene (BaP) and bind reactive BaP intermediates to hepatic DNA indicate that biochemical differences in the metabolism of carcinogenic PAHs may explain, at least in part, the apparent lower susceptibility of starry flounder than English sole to chemically induced hepatocarcinogenesis.

Animals↗

PubMed2005

Isolation of DNA from plants with large amounts of secondary metabolites.

Many plant species have high contents of polysaccharides, polyphenols, or other secondary metabolites that can interfere with DNA extraction and purification. These contaminating compounds can lead to poor DNA yield and prevent access by modifying enzymes, such as restriction endonucleases and Taq polymerase. A number of factors, including choice of plant tissue, tissue preparation, and modifications of the extraction buffer, can help in DNA extraction for difficult plant species. This chapter presents some of the DNA extraction protocols developed for various plants.

DNA, Plant↗

PubMed1994

Association of single-stranded transferred DNA from Agrobacterium tumefaciens with tobacco cells.

During the inception of crown gall tumorigenesis, the transferred DNA (T-DNA) is processed from the Ti (tumor inducing) plasmid of Agrobacterium tumefaciens and is transferred to plant cells. T-DNA processing and transfer require the induction of vir (virulence) genes by phenolic compounds secreted by wounded plant cells. After vir gene induction, both single-stranded (T-strands) and double-stranded forms of processed T-DNA accumulate in the bacteria. Although current models favor the transfer of T-strands to plants, there has yet been no experimental evidence to show this. In this paper, we show that T-strands disappear from acetosyringone-induced A. tumefaciens within 30 min of bacterial cocultivation with tobacco protoplasts. PCR analysis of T-DNA associated with protoplasts indicates that single-stranded, but not double-stranded, T-DNA can be detected in the plant cells within 30 min of bacterial cocultivation. Control experiments show that this T-DNA does not originate from lysed contaminating bacterial cells. T-DNA transfer depends on a functional bacterial virB operon. Protoplast infections using an A. tumefaciens virE mutant result in a low level of accumulation of T-strands in the plant cells.

Agrobacterium tumefaciens↗

PubMed1984

Varicella-zoster virus-induced transformation of mammalian cells in vitro.

A mixture of varicella-zoster virus-infected human embryonic lung fibroblasts and hamster embryo cells produced foci of morphologically transformed cells after several weeks of incubation. These transformed cells exhibited virus-specific antigens by immunofluorescence and developed surface Fc receptors. They induced aggressive fibrosarcomas when injected back into inbred hamsters. Cells derived from hamster tumor tissue exhibited similar properties. The tumor-bearing hamsters develop antibodies specific for varicella-zoster virus (VZV) antigens. Cell lines derived from both the original transformants and explanted hamster tumor tissue have varying growth properties. All maintain indefinite growth. All eventually lose varicella-zoster virus-specific immunofluorescence. None retain VZV-specific DNA sequences as determined by dot blot and Southern blot hybridization using radiolabeled whole VZV DNA and cloned VZV DNA fragments as a probe. A few transformed and tumor cell lines frozen relatively soon after isolation and stored in liquid nitrogen were also thawed, replicated to mass culture, and analyzed for VZV-specific DNA sequences. Hybridization with radiolabeled whole VZV DNA initially suggested that some of these cell lines did contain virus-specific DNA sequences. However, hybridization with cloned VZV DNA fragments radiolabeled in vitro and representing greater than 95% of the virus genome was negative. Karyotyping of these "positive" transformed cells indicated that they are of human and not hamster origin. The positive hybridization with whole VZV DNA therefore most likely represented contamination of the probe by host DNA sequences. The cells that survived freezing then were predominantly transformants of human origin. Attempts to repeat the transformation of hamster embryo and baby hamster kidney cells with laboratory-passaged VZV strains have been unsuccessful. Similarly, we have been unable to transform cells with whole VZV DNA or cloned VZV DNA fragments, although whole VZV DNA is demonstrably infectious. Apparently, transformation of cells by the varicella-zoster virus is a very rare event and one that may require a recent clinical isolate. Fresh clinical isolates of varicella-zoster virus are seemingly able to transform mammalian cells in vitro. The transformed cells have malignant properties and are capable of indefinite growth. Although VZV gene function can be detected early after transformation, there is no evidence that a VZV-specific protein product is required. Transformation of mammalian cells by varicella-zoster virus apparently occurs through a "hit-and-run" mechanism.

Animals↗