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Results for “DNA Contamination”

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At least 847 records · Page 47Linked to original sources

PubMed1994

Co-purification of gastric mucoproteins with DNA: an explanation for the reported 'interaction' of omeprazole with DNA in rat tissues.

Recently, Phillips et al. reported that small amounts of radioactivity derived from [14C]omeprazole were 'associated' with DNA purified from gastrointestinal tissues of treated rats (Mutagenesis 7, 277-283, 1992). We hypothesized that this radioactivity arose from omeprazole bound to contaminating protein in the DNA fraction (Mutagenesis 7, 395-396, 1992). Using rats injected with 35S-labeled amino acids, we found significant protein contamination (0.06 microgram of protein per microgram of DNA) in DNA purified from gastrointestinal tissues. Gastric mucous proteins represent likely candidates for binding of omeprazole in the rat model used by Phillips et al. To investigate this, we partially purified proteins from gastric mucus, incubated them with [14C]omeprazole, and then added these radiolabeled mucoproteins to homogenates of rat colon and duodenum before starting the DNA purification. Detectable amounts of the added mucoproteins remained in the DNA fraction, but none of the control protein, bovine serum albumin, remained with the DNA. Further characterization of the mucoproteins by hydroxyapatite chromatography indicated that a certain population of these proteins survived the DNA purification procedures. These data indicate that the association of omeprazole with DNA reported by Phillips et al. most probably is explained by binding of omeprazole to mucous glycoproteins (or other proteins present in the GI tract) that selectively survive DNA purification protocols.

Amino Acids↗

PubMed1990

Evaluation of different hybridization procedures for the detection of mycoplasma contamination in cell cultures.

Cell culture samples were analysed for mycoplasma contaminations with two different DNA probes which have been described earlier. One probe (the H900 probe), derived from the 23S rRNA gene of Mycoplasma hyorhinis, cross-hybridized with virtually all mycoplasmas (including the acholeplasmas). The other probe (the T2 probe), derived from a protein gene of Acholeplasma laidlawii, cross-hybridized with most acholeplasmas. The two probes were compared in three different direct filter hybridization procedures without previous isolation of DNA or RNA. One of the procedures, developed in the present study, gave the highest sensitivity in DNA-RNA hybridization but also worked satisfactorily in DNA-DNA hybridization. The sensitivity of the H900 probe in filter hybridization experiments was compared with the sensitivity of a commercial probe for detection of mycoplasma contaminations in cell cultures. The H900 probe was found to be at least 25 times more sensitive for all cell culture mycoplasmas except for A. laidlawii, for which they were equally sensitive.

Animals↗

PubMed1997

Predictive value of genetic diagnosis for cancer micrometastasis: histologic and experimental appraisal.

BACKGROUND: The recently introduced genetic diagnosis of cancer micrometastasis is quite attractive because of its high detection sensitivity. Not infrequently, however, there are marked discrepancies between genetic and conventional histologic diagnoses, especially concerning lymph nodes from colon carcinoma patients. Because the histologic approach has long been relied on in the clinic, the reasons for the differences in results need to be elucidated. METHODS: Serial sections of genetic diagnosis positive but histologic negative lymph nodes of colon carcinoma patients were prepared for histologic and immunohistochemical studies. To investigate the possible contaminating influence of DNA sequences derived from degraded carcinoma cells from the primary site through the lymphatics, the authors also injected purified DNA of human colon carcinoma cells (SW480) into the foot pads of rats and sequentially examined lymph nodes using genetic diagnosis methodology. RESULTS: Careful histologic examination of genetic diagnosis positive, histologically negative lymph nodes of colon carcinoma patients confirmed the absence of cancer cells, whereas p53 protein was immunohistochemically demonstrated to be present in the cytoplasm of sinus histiocytes. In the rat experiment, positive reactions were obtained with the inguinal lymph nodes beginning 30 minutes after the injection, and lymph nodes at various sites were subsequently affected, even after a 72-hour period. CONCLUSIONS: The current study thus suggests that positive results with genetic diagnosis may simply indicate the presence of tumor DNA and do not necessarily mean that viable cancer cells are present. Although the genetic approach may still hold promise for the detection of cancer micrometastases, its predictive value should be carefully assessed clinicopathologically, because its supersensitivity may be associated with a greatly increased false-positive rate.

Animals↗

PubMed1999

Molecular prenatal diagnosis of ataxia telangiectasia heterozygosity by direct mutational assays.

Ataxia telangiectasia (AT) is a severe autosomal recessive disease, rare but not infrequent in Italy. Owing to the seriousness of the disease, prenatal diagnosis has been attempted in the past by means of cytogenetic, biochemical, radio-biological and indirect molecular analyses. We performed the first direct molecular prenatal diagnosis of AT on a chorionic villi sample from a 37-year-old woman at the 10th week of pregnancy. She had two previous children suffering AT and two induced abortions. At molecular analysis her affected children were compound heterozygotes for mutations 7792C-->T in exon 55 (from the mother) and 8283delTC in exon 59 (from the father). The prenatal diagnosis was performed by two different operators in double-blind form. Mutation 7792C-->T was studied by restriction enzyme analysis using TaqI. Mutation 8283delTC was screened by heteroduplex analysis. The fetus was heterozygous for the mutation 7792C-->T (confirmed by sequencing). In order to verify the possible contamination by maternal DNA, polymorphic loci HLA-DRB1 and HLA-DQA1, together with microsatellite markers D6S259, D11S2000, D11S29, D11S1778 and D11S2179, were examined. All these loci were informative, showing that the fetus received only one allele from each parent. The heterozygosity for ATM mutation 7792C-->T was confirmed by molecular studies after the birth of a healthy male baby.

Adult↗

PubMed2004

Early population differentiation in extinct aborigines from Tierra del Fuego-Patagonia: ancient mtDNA sequences and Y-chromosome STR characterization.

Ancient mtDNA was successfully recovered from 24 skeletal samples of a total of 60 ancient individuals from Patagonia-Tierra del Fuego, dated to 100-400 years BP, for which consistent amplifications and two-strand sequences were obtained. Y-chromosome STRs (DYS434, DYS437, DYS439, DYS393, DYS391, DYS390, DYS19, DYS389I, DYS389II, and DYS388) and the biallelic system DYS199 were also amplified, Y-STR alleles could be characterized in nine cases, with an average of 4.1 loci per sample correctly typed. In two samples of the same ethnic group (Aonikenk), an identical and complete eight-loci haplotype was recovered. The DYS199 biallelic system was used as a control of contamination by modern DNA and, along with DYS19, as a marker of American origin. The analysis of both mtDNA and Y-STRs revealed DNA from Amerindian ancestry. The observed polymorphisms are consistent with the hypothesis that the ancient Fuegians are close to populations from south-central Chile and Argentina, but their high nucleotide diversity and the frequency of single lineages strongly support early genetic differentiation of the Fuegians through combined processes of population bottleneck, isolation, and/or migration, followed by strong genetic drift. This suggests an early genetic diversification of the Fuegians right after their arrival at the southernmost extreme of South America.

Argentina↗

PubMed1990

Human natural killer cells and mature T lymphocytes express identical CD3 zeta subunits as defined by cDNA cloning and sequence analysis.

In order to characterize the CD3 zeta-related protein found in human natural killer (NK) cells and compare it with CD3 zeta expressed in T lymphocytes, the present study was performed. A polyclonal CD3-CD16+NK population displaying a strong non-major histocompatibility complex-restricted cytotoxic activity against the NK target K-562 was isolated and a product corresponding to CD3 zeta amplified using the polymerase chain reaction method. This 0.6-kb product was present in similar amounts in NK cells and T cells. In contrast, a product corresponding to CD3 delta was amplified from T lymphocytes exclusively. Thus, the CD3 zeta product detected in NK cells did not originate from contaminating T cells. DNA sequence analysis of two independent polymerase chain reaction products from the NK cells demonstrates that human NK cells and mature T cells share a CD3 zeta subunit with an identical primary amino acid sequence. The nucleotide sequence of a third NK-derived cDNA revealed an insertion of a CAG triplet encoding an additional glutamine residue in the cytoplasmic domain. Since this residue is encoded by nucleotides at a putative RNA splice junction, it possibly results from a difference in pre-mRNA splicing. Taken together, these data show that CD3 zeta is not structurally distinct in NK cells and in T lymphocytes.

Amino Acid Sequence↗

PubMed1995

Expression and tissue localization of donor-specific complement C3 synthesized in human renal allografts.

Recent evidence suggests that the third component of complement, C3, is synthesized in renal tissue, and that increased C3 synthesis occurs in allograft rejection and immune complex-mediated nephritis. However, it is unclear whether intrinsic renal cells or migratory cells in the inflammatory infiltrate, possibly of recipient bone marrow origin, are the source of the C3 detected. This was investigated by determining the C3 allotypes of mRNA and protein produced by transplanted human kidney. Twenty donor-recipient pairs were examined, of which nine pairs had C3 allotypes that were informatively mismatched at the C3 F/S locus. Reverse transcriptase polymerase chain reaction (RT-PCR) followed by amplification refractory mutation system analysis showed intracellular donor-specific mRNA expression in six of these nine cases, at up to 61 days post-transplantation. Nested PCR reactions and the size of PCR products excluded contamination by genomic DNA. Allotype-specific staining of frozen sections of renal cortex demonstrated donor-derived C3 protein in both glomeruli and tubules of all biopsies examined, in a predominantly tubular distribution. These results imply that at least some of the pro-inflammatory effects of complement arise from intrinsic tissue synthesis of donor C3, and that this may represent a previously unrecognized source of tissue injury. The occurrence of local synthesis of C3 of donor allotype may have functional implications related to C3 allotype, and may also be relevant to strategies to inhibit intrarenal complement-mediated injury.

Alleles↗

PubMed1977

Embryotoxic effects of heterologous antisera against rat Reichert's membrane.

Parietal yolk-sacs of rat embryos at the fifteenth day of gestation were obtained by microdissection. A Reichert's membrane (RM) preparation was isolated by treating the parietal yolk-sacs with the chelating agent tetrasodium salt of ethylenediaminetetraacetic acid (EDTA) combined with mechanical shaking. Less than 1% of the membrane preparation was DNA and phosphorus contaminants. The membrane purity was also evaluated by electrom microscopic examination. Rabbit Ig G directed against the RM preparation when injected ip into ninth day pregnant rats produced malformations, fetal growth retardation and resorption. Fluorescent-labeled antibody localization studies demonstrated that the teratogenic antibodies localized in RM. It is postulated that RM antibodies induce teratogenesis by interfering with the function of RM.

Animals↗

PubMed2000

Quality control and optimized procedure of hybridization capture-PCR for the identification of Mycobacterium avium subsp. paratuberculosis in faeces.

Nucleic acid sequence capture techniques are used to improve both the sensitivity and specificity of PCR for the diagnosis of plant, animal and human diseases. Hybridization capture-PCR (HC-PCR) was first reported as a method for the detection of Mycobacterium avium subsp. paratuberculosis in 1995 and was successfully trialed on a small number of faecal samples from cattle with Johne's disease. A locally optimized HC-PCR method was evaluated on faeces from infected and non-infected animals. However, sample to sample cross contamination during the DNA purification step highlighted that the original format of the test was unsuitable for routine diagnostic use. Here, we report modifications and optimization of HC-PCR, particularly with respect to DNA purification from faeces, hybridization and capture steps. We also identified procedurally sensitive critical points in the test during capture and washing of magnetic beads. Southern blotting was omitted from the protocol to preserve specificity but this resulted in analytical sensitivity of 5000 organisms per 200 mg faecal sample. Nevertheless, HC-PCR detected M.paratuberculosis in pellets from infected sheep diluted at rates of up to 1 in 100 in normal faeces, suggesting that the technique should be evaluated further for low-cost diagnosis in flocks/herds using pooled samples.

Animals↗

PubMed1993

Lack of evidence supporting the presence of mRNA for the thyrotropin receptor in extra-ocular muscle.

The search for autoantigenic targets in thyroid associated ophthalmopathy (TAO) and a possible link with the thyroid continues. Several authors have presented data suggesting that extrathyroidal tissues, e.g. extraocular muscle (EOM), may contain a functional thyrotropin receptor (TSH-R). We have applied Northern blotting and PCR amplification in an attempt to demonstrate the mRNA for the TSH-R in EOM, which although predominantly composed of muscle, may contain a significant proportion of fibroblasts. In Northern blots of poly(A) mRNA of normal human thyroid, EOM and skeletal muscle (SM) probed with a p32 labeled hTSH-R cDNA, transcripts of 4.6 and 4.4 kb were observed only in the thyroid. PCR amplification was performed on thyroid and EOM cDNAs using pairs of primers designed to amplify exons 1-->9, the extracellular domain (ECD), and exon 10, the intracellular domain (ICD). Both the ECD and ICD were amplified from a thyroidal cDNA library but only the ICD in the EOM cDNA library, this probably being due to the inevitable contamination with genomic DNA. These results do not support the hypothesis that the TSH receptor, as such, would be an autoantigen of EOM involved in TAO.

Adipose Tissue↗

PubMed2002

Paternity testing after pregnancy termination using laser microdissection of chorionic villi.

We report an unusual case of paternity testing from residues of chorionic villi 5 weeks after pregnancy termination. The autopsy of a 32-year-old female homicide victim revealed the presence of intact chorionic villi at the former placenta implantation site. Fetal cells were selectively isolated by laser-induced microdissection of the remaining villi to avoid contamination with maternal DNA. Simultaneous amplification of 12 STR loci in 2 PCR reactions resulted in a combined probability of paternity of 99.94%. This case demonstrates that laser-assisted microdissection and multiplex STR typing provide tools for paternity testing performed on endometrial mucosa long after the product of conception was removed by therapeutic abortion.

Abortion, Induced↗

PubMed2005

Species and sex identification of western lowland gorillas (Gorilla gorilla gorilla), eastern lowland gorillas (Gorilla beringei graueri) and humans.

Methods for the identification of the sex and species of individuals from samples non-invasively taken from humans and gorillas were established. Amplification of a segment of amelogenin (AMG), which is an X-Y homologous gene, using two pairs of primers from human AMG, revealed both X- and Y-specific bands. The possibility of sex identification was examined by typing the AMG gene using hair and fecal samples from captive western lowland gorillas (Gorilla gorilla gorilla) in Japan and hair samples from wild eastern lowland gorillas (Gorilla beringei graueri) in the Kahuzi-Biega National Park, Democratic Republic of Congo, which were sexed by direct observation. Species-specific bands of AMG in gorillas and humans were identified by restriction fragment length polymorphisms analysis. These tests could be used for sexing unidentified individuals of wild western and eastern lowland gorillas, and screening contamination of human DNA from non-invasively acquired samples.

Amelogenin↗

PubMed1985

C1q binding to mitochondria: a possible artefact?

Mitochondrial preparations, obtained from human tonsils and from rat spleen, liver, heart, and kidney tissues, bound [125I]C1q with affinities of 10(7)-10(8)M-1. The binding of C1q was not affected by treatment of the mitochondrial preparations with pronase, trypsin, or phospholipase D, but it was lowered 5-6-fold following treatment of the mitochondria with DNase and RNase. Binding of C1q to mitochondrial preparations was also greatly diminished by limited chemical modification of C1q with cyclohexane-1,2-dione. It is suggested that the reported binding of C1q to mitochondria may have arisen from the protein binding to DNA and/or RNA contaminating the mitochondrial preparations.

Animals↗

PubMed1985

Mutagenicity testing of water with fish: a step forward to a reliable assay.

A step forward has been set towards the realization of a reliable "sister-chromatid" exchange (SCE) assay with fish for the detection of mutagens in water. This test can detect mutagenic contaminants in water without prior concentration steps. A healthy breeding stock of the tropical fish Nothobranchius rachowi has been set up in our laboratory. This fish is particularly suited for the SCE assay because of its low number of chromosomes. The major improvement consisted of the development of a reliable staining technique for the differentiation of sister-chromatids. The assay can now be used for research purposes. With a few improvements it can become a rapid low-cost test for the screening of effluents on contamination with DNA-damaging agents.

Animals↗

PubMed2005

Denaturing RNA electrophoresis in TAE agarose gels.

Current methods of analytical RNA electrophoresis are based on the utilization of either complicated laboratory instrumentation or toxic, carcinogenic, or expensive chemicals. We suggest here the use of classical Tris-acetate-ethylenediamine tetraacetic acid (TAE) agarose gels combined with prior denaturation of RNA samples in hot formamide for the electrophoretic separation of RNA species. We present a brief comparison of the proposed TAE/formamide method with the most common 3-(N-morpholino)propanesulfonic acid/formaldehyde agarose gel protocol and show that both methods produce comparable results for size determination of RNA molecules and subsequent Northern blotting of gels. In addition to purified RNA samples, the robustness of the TAE/formamide protocol is demonstrated by its suitability for the analysis of RNA quality in crude yeast cell lysates containing large amounts of proteins, DNA, and other contaminating molecules. We therefore propose the TAE/formamide agarose electrophoresis as a rapid, simple, and cheaper alternative to current methods of RNA electrophoresis. Additionally, another benefit is the reduced exposure of laboratory personnel to hazardous chemicals.

Acetates↗

PubMed2005

Downstream processing of MDCK cell-derived equine influenza virus.

A microcarrier-based process was used to produce equine influenza virus (A/Equi 2 (H3N8), Newmarket 1/93) in Madin Darby Canine kidney (MDCK) cells. The virus was purified in a sequence of downstream processing steps comprising of depth filtration, inactivation, ultrafiltration (UF) and gel filtration. In the ultrafiltration step, the hemagglutinin (HA) was recovered to 100%. A high increase of neuraminidase (NA) activity indicated the removal of some inhibitory compounds during this step. At the same time, the level of contaminating proteins and DNA was reduced by more than 88%. In the subsequent size exclusion chromatography (Sepharose CL 2B), the recovery of HA and NA in the "virus peak" was 37.8 and 59.8%, respectively compared to the concentrated feed material. Inconsistencies in the overall mass balance for HA and NA (70.0 and 69.2%) during gel filtration indicated non-specific interactions of the inactivated virus to the gel matrix which is supported by a HA recovery of about 50% in shake flask experiments performed as a control. Overall 35.8% of HA and 291.6% of NA were recovered. More than 95.7% of the host cell proteins and 98.7% of the host cell DNA were removed during downstream processing.

Animals↗

PubMed2005

Rapid and reliable real-time PCR assay for detection of the macrolide efflux gene and subsequent discrimination between its distinct subclasses mef(A) and mef(E).

A real-time PCR assay is described for detection of the macrolide efflux gene, mef. Following amplification, unambiguous discrimination between the two mef subclasses, mef(A) and mef(E), is easily established using a melting curve analysis. The results of this novel assay were 100% concordant with a conventional PCR-RFLP approach but requires far less hands-on time. Furthermore, the real-time format offers semiquantitative results allowing identification of contaminated cultures and/or DNA preparations.

Bacterial Proteins↗

PubMed1989

Practical considerations in the production, purification, and formulation of monoclonal antibodies for immunoscintigraphy and immunotherapy.

Issues associated with the large-scale production of monoclonal antibodies for pharmaceutical applications are examined. The development of a commercial monoclonal antibody production process involves much more than just scaling-up the laboratory process and making it cost-effective. It involves establishing the hybridoma cell bank with cells that are free of adventitious agents such as viruses and mycoplasma, that have stability in continuous culture for antibody-production rate and cell viability, and that do not have unusual or expensive media requirements. The style and mode of operation of the bioreactor used to produce the antibody must be explored. The antibody-based product must be processed to high levels of purity, and specific contaminants such as DNA and endotoxin must be reduced to extremely low levels. Appropriate labeling or drug conjugation chemistries must also be developed. The product must be formulated so that it has performance characteristics that are stable over a reasonable period of time. Adequate test procedures must be developed to assure product purity, activity, stability, and safety on a lot-to-lot-basis. Compliance with federal regulations, guidelines, and procedures must be guaranteed. In the coming decade, it is likely that the two arms of biotechnology, hybridoma technology and recombinant DNA technology, will be used together to generate unique protein molecules. These new reagents will face the same practical considerations summarized in this review.

Animals↗