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Results for “DNA Contamination”

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At least 703 records · Page 39Linked to original sources

PubMed1995

Flow and image cytometric DNA measurements in fine needle aspiration samples of prostatic neoplasms.

OBJECTIVE: To compare the DNA content measured by flow cytometry (FCM) and image analysis (IA) from prostatic fine needle aspiration (FNA) samples. STUDY DESIGN: A total of 48 samples were studied. FCM was performed on propidium iodide-stained nuclei according to the Vindelov method, and image analysis was performed on Feulgen-stained slides. Positive FNA results were grade (1-3) and compared with Gleason grades. RESULTS: Aneuploidy was closely related to positive FNA results (P < .01). DNA histograms were found to be aneuploid in all grade 3 carcinomas (n = 13) by IA and in 11 cases (84.6%) by FCM. Grade 2 carcinomas (n = 9) were found to be aneuploid with both methods. In grade 1 carcinomas (n = 10), 2 cases exhibited IA aneuploid profiles, whereas all FCM cases were diploid. Aneuploid profiles were more often associated with high Gleason scores than were diploid ones (P < .01). Among the 16 patients with negative FNA results, two cases had tetraploid DNA profiles related to contaminating seminal vesicle cells. The difference in DNA measurements reached 10.4% but was not statistically significant. CONCLUSION: These findings show that the two methods, as applied to prostatic FNA samples, give comparable results and that seminal vesicle cells may be responsible for false tetraploid profiles.

Biopsy, Needle↗

PubMed1998

Investigation of cross contamination in a Mycobacterium tuberculosis laboratory using IS6110 DNA fingerprinting.

SETTING: A laboratory for routine culturing of Mycobacterium tuberculosis. OBJECTIVE: Investigation of an episode of laboratory cross contamination using IS6110 restriction fragment length polymorphism (RFLP) typing. Improvement of laboratory protocols to prevent contaminations in the future. To stress the importance of 'good laboratory practice', and interaction with clinicians about laboratory results. DESIGN: Fingerprinting of mycobacterial isolates from 1) cultures suspected of being contaminated and 2) strains suspected of being the source of the cross-contamination. RESULTS: RFLP typing results indicated that clinical samples were contaminated by strains which had been processed in species identification procedures one day earlier in the same safety cabinet. This cross contamination also resulted in exceptional RFLP typing results--mixed banding patterns. Three patients were treated on the basis of false-positive laboratory results. Because the laboratory results were confusing for the clinicians, the treatment of one true tuberculosis patient was severely delayed. CONCLUSION: 'Good laboratory practice' is very important to prevent cross contamination. RFLP typing proved to be a useful tool to trace the source of contamination. Interaction with clinicians receiving doubtful results is of the utmost importance.

Bacterial Typing Techniques↗

PubMed1992

Preclinical models for human pre-embryo biopsy and genetic diagnosis. II. Polymerase chain reaction amplification of deoxyribonucleic acid from single lymphoblasts and blastomeres with mutation detection.

OBJECTIVE: To demonstrate the use of the polymerase chain reaction in the amplification of deoxyribonucleic acid (DNA) from single human lymphoblasts and mouse blastomeres. Amplified target genes for diagnosis of sickle cell anemia and Tay-Sachs are shown. Similarly, the sparce fur mouse model for ornithine transcarbamylase deficiency was used as an X-linked system for demonstration of mutation detection after biopsy of a single blastomere. A new diagnostic method for the detection of the ornithine transcarbamylase mutation using the restriction enzyme Mse I is presented. Accuracy and reproducibility were assured. DESIGN: Polymerase chain reaction proficiency test for amplification from single cells was studied. Also, accuracy of mutation detection systems was demonstrated. SETTING: Laboratories of The Jones Institute for Reproductive Medicine, Department of Obstetrics and Gynecology, Eastern Virginia Medical School. PATIENTS, PARTICIPANTS: We used the sparse fur mouse model and human blood cells. INTERVENTIONS: Pre-embryo biopsy, polymerase chain reaction amplification, and mutation detection were performed. MAIN OUTCOME MEASURES: Accuracy and reproducibility of DNA amplification without contamination, as well as efficient diagnostic analysis, from both single somatic and embryonic cells were shown. RESULTS: DNA amplification from single cells was uniformly rapid (6 to 10 hours) reproducible (n = 220) and accurate (n = 52). CONCLUSIONS: Our findings support the feasibility of clinical application for pre-embryo biopsy and genetic diagnosis of specific heritable diseases.

Amino Acid Sequence↗

PubMed1978

Preparation of chromatin containing ribosomal deoxyribonucleic acid from the macronucleus of Tetrahymena pyriformis.

A method is described that enables a chromatin fraction containing ribosomal DNA (DNA containing sequences coding for rRNA) to be prepared from the macronuclei of growing or stationary cultures of Tetrahymena pyriformis. This material is obtained in yields of between 25 and 75% of the theoretical maximum. The DNA in this fraction was identified as ribosomal DNA on the basis of its density and molecular weight, and it appears not to be appreciably contaminated by other DNA. The method relies on the approximate assumption that ribosomal DNA is the smallest species of DNA in chromatin in the nucleus, and avoids the use of mechanical force, or enzyme action, to fractionate chromatin.

Animals↗

PubMed2025

LYCEUM: learning to call copy number variants on low-coverage ancient genomes.

MOTIVATION: Copy number variants (CNVs) are pivotal in driving phenotypic variation that facilitates species adaptation. They are significant contributors to various disorders, making ancient genomes crucial for uncovering the genetic origins of disease susceptibility across populations. However, detecting CNVs in ancient DNA (aDNA) samples poses substantial challenges due to several factors: (i) aDNA is often highly degraded; (ii) contamination from microbial DNA and DNA from closely related species introduces additional noise into sequencing data; and finally, (iii) the typically low-coverage of aDNA renders accurate CNV detection particularly difficult. Conventional CNV calling algorithms, which are optimized for high-coverage read-depth signals, underperform under such conditions. RESULTS: To address these limitations, we introduce LYCEUM, the first machine learning-based CNV caller for aDNA. To overcome challenges related to data quality and scarcity, we employ a two-step training strategy. First, the model is pre-trained on whole genome sequencing data from the 1000 Genomes Project, teaching it CNV-calling capabilities similar to conventional methods. Next, the model is fine-tuned using high-confidence CNV calls derived from only a few existing high-coverage aDNA samples. During this stage, the model adapts to making CNV calls based on the downsampled read depth signals of the same aDNA samples. LYCEUM achieves accurate detection of CNVs even in typically low-coverage ancient genomes. We also observe that the segmental deletion calls made by LYCEUM show correlation with the demographic history of the samples and exhibit patterns of negative selection inline with natural selection. AVAILABILITY AND IMPLEMENTATION: LYCEUM is available at https://github.com/ciceklab/LYCEUM.

DNA Copy Number Variations↗

PubMed1992

In-cell PCR from mRNA: amplifying and linking the rearranged immunoglobulin heavy and light chain V-genes within single cells.

We describe a process for the identification of mRNAs within single cells, as demonstrated with the immunoglobulin (Ig) variable region (V) genes of two mouse hybridoma cell lines and the bcr-abl fusion gene of the human K562 myeloid leukaemia line. The cells were fixed and permeabilised, the mRNA reverse transcribed to cDNA and the cDNA amplified by the polymerase chain reaction (PCR). After using fluorescent PCR primers, the amplified DNA could be detected within the cells as demonstrated by confocal fluorescence microscopy and flow cytometry. Furthermore the amplified Ig VH and VL DNA could be assembled within the same cell using suitable PCR primers. We detected no cross-contamination of amplified DNA between cells: the DNA isolated from mixtures of two hybridoma cell lines (B1-8 and NQ10/12.5) treated to in-cell PCR and assembly, was shown by cloning to correspond to the combinations of VH and VL genes of the parent hybridomas. We forsee diverse applications of in-cell assembly by PCR, especially for the analysis of the combinations of chains of rearranged Ig or T cell receptor (TCR) V-genes in a population of cells, and the construction of human antibodies from the V-genes of immune B-lymphocytes.

Animals↗

PubMed1990

A bacteriophage lambda DNA purification procedure suitable for the analysis of DNA from either large or multiple small lysates.

A method for the efficient preparation of high quality bacteriophage lambda DNA from cleared lysates is described. Advantages of the method include high DNA yields (typically around 0.8 micrograms of DNA/1 ml of cleared lysate), speed of processing (approximately 2 h from lysate to DNA), economy, and the absence of any requirement for phenol or chloroform extractions. The technique involves the concentration of phage particles by standard polyethylene glycol precipitation followed by enzymatic treatment to remove contaminating RNA and DNA. Phage particles are then lysed with sodium dodecyl sulfate (SDS) at elevated pH and temperature. Contaminating protein/SDS complexes are rendered insoluble by the addition of potassium acetate and removed by centrifugation. The quality of the resultant DNA is comparable to that prepared by cesium chloride banding for all standard molecular biological purposes providing that spermidine is included in all restriction endonucleases digestions.

Acetates↗

PubMed2004

Application of the BioMek 2000 Laboratory Automation Workstation and the DNA IQ System to the extraction of forensic casework samples.

Robotic systems are commonly utilized for the extraction of database samples. However, the application of robotic extraction to forensic casework samples is a more daunting task. Such a system must be versatile enough to accommodate a wide range of samples that may contain greatly varying amounts of DNA, but it must also pose no more risk of contamination than the manual DNA extraction methods. This study demonstrates that the BioMek 2000 Laboratory Automation Workstation, used in combination with the DNA IQ System, is versatile enough to accommodate the wide range of samples typically encountered by a crime laboratory. The use of a silica coated paramagnetic resin, as with the DNA IQ System, facilitates the adaptation of an open well, hands off, robotic system to the extraction of casework samples since no filtration or centrifugation steps are needed. Moreover, the DNA remains tightly coupled to the silica coated paramagnetic resin for the entire process until the elution step. A short pre-extraction incubation step is necessary prior to loading samples onto the robot and it is at this step that most modifications are made to accommodate the different sample types and substrates commonly encountered with forensic evidentiary samples. Sexual assault (mixed stain) samples, cigarette butts, blood stains, buccal swabs, and various tissue samples were successfully extracted with the BioMek 2000 Laboratory Automation Workstation and the DNA IQ System, with no evidence of contamination throughout the extensive validation studies reported here.

Automation↗

PubMed2004

Effect of comprehensive validation of the template isolation procedure on the reliability of bacteraemia detection by a 16S rRNA gene PCR.

The influence of the DNA extraction method on the sensitivity and specificity of bacteraemia detection by a 16S rRNA gene PCR assay was investigated. The detection limit of the assay was 5 fg with purified DNA from Escherichia coli or Staphylococcus aureus, corresponding to one bacterial cell. However, with spiked blood samples, the detection limits were 10(4) and 10(6) CFU/mL, respectively. The sensitivity of the S. aureus assay was improved to the level of the E. coli test with the addition of proteinase K to the commercial DNA extraction kit protocol. Ten (16.6%) of 60 amplification reactions were positive with templates isolated from sterile blood, while PCR reagent controls were negative, thereby indicating contamination during the DNA extraction process. Blood samples were spiked with serial dilutions of E. coli and S. aureus cells, and six PCR results were obtained from three extractions for each blood sample. A classification threshold system was devised, based on the number of positive reactions for each sample. Samples were deemed positive if at least four positive reactions were recorded, making it possible to avoid false-positive results caused by contamination. These results indicate that a comprehensive validation procedure covering all aspects of the assay, including DNA extraction, can improve considerably the validity of PCR assays for bacteraemia, and is a prerequisite for the meaningful detection of bacteraemia by PCR in the clinical setting.

Bacteremia↗

PubMed2006

Detection of HIV-1 in injection paraphernalia: risk in an era of heightened awareness.

Links between AIDS and self-injection of drugs were first recognized more than 20 years ago, but identification of a specific pathogen and ways to neutralize it has not led to complete success in preventing transmission of HIV-1 infection among injecting drug users (IDUs). A street ethnographer identified active risk locales (places where IDUs go to inject drugs) and recruited their proprietors into a study of contaminated injection paraphernalia. Collected paraphernalia from locales were analyzed for contamination by HIV-1 using real-time polymerase chain reaction (PCR). Proprietors and clientele of 16 risk locales participated by contributing used paraphernalia and/or agreeing to a blood test (0.5-1 mL drawn by finger stick). Realtime PCR was the primary measure used to determine contamination of injection paraphernalia and blood samples with HIV-1. Of 130 samples collected at baseline, a total of 8 were found to have evidence of HIV-1 contamination by detection of either HIV-1 RNA or DNA. The most serious contamination (up to 600,000 copies per milliliter) was found in ancillary paraphernalia, rather than needle/syringe (N/S) specimens. Only 4 of 74 N/S specimens had any evidence of HIV-1 contamination at all (with very low viral loads), and none had both HIV-1 DNA and RNA. Although IDUs in risk locales in Miami/Dade appear to be taking care of their N/S with regard to contamination by HIV-1, important evidence of contamination in ancillary paraphernalia, especially cookers and cottons, indicates that IDUs may still incur serious risk regardless of how well they care for their N/S. Our observations indicated that IDUs rinsed their N/S before returning them to the proprietors, from whom we eventually collected them, and this rinsing would have masked the contamination to which they were exposed through use of unrinsed cookers and reused cottons.

Anthropology, Cultural↗

PubMed1997

Intracellular delivery of lipopolysaccharide during DNA transfection activates a lipid A-dependent cell death response that can be prevented by polymyxin B.

The presence of lipopolysaccharide (LPS) as a contaminant in plasmid DNA prepared from Escherichia coli is well documented, and we have previously demonstrated that LPS internalization during adenovirus-mediated gene transfer can generate a toxicity in some primary cell types. We demonstrate here that in addition to adenoviral systems, several commonly used nonviral methods of gene transfer also activate this cell death response in the presence of LPS. Subcomponents of LPS were analyzed and the toxicity was found to be due to the lipid A component of LPS. The LPS-chelating antibiotic polymyxin B, when present at concentration of 10-30 micrograms/ml, can block this toxicity.

Anti-Bacterial Agents↗

PubMed1995

The use of in vitro DNA adduct formation to estimate the genotoxicity of residues at contaminated sites.

Genotoxic carcinogens such as polycyclic aromatic hydrocarbons (PAHs) covalently bind to the bases in DNA to form adducts. The formation of DNA adducts is significant with respect to chemical carcinogenesis. Many contaminated sites contain quantities of carcinogens such as PAHs, and the evaluation of the genotoxicity of these soils has important implications for human risk assessment. DNA adducts can be formed using an in vitro system incorporating extracts from contaminated soils. The 32P-postlabelling assay is a sensitive technique for the detection of DNA adducts from complex mixtures of environmental carcinogens. These techniques have been used to form and detect DNA adducts using soils from a number of coal gasworks sites. The results show that the extent of adduct formation depends partially on the petroleum hydrocarbon content of samples, but also on other undetermined factors related to composition. While environmental weathering has been shown to effect the PAH composition of samples, this is not an important factor in controlling the genotoxicity of samples as estimated by DNA adduct formation.

Animals↗

PubMed1990

Detection of hepatitis B virus DNA in serum by polymerase chain reaction. Application for clinical diagnosis.

Standard methods of virus DNA detection using the polymerase chain reaction can be time consuming and can involve multiple steps in which contamination with exogenous DNA can occur. Therefore, we developed a simplified method for detecting hepatitis B virus DNA in serum. The main advantages of this method are that it can be performed rapidly, consists of only several steps, and has a false positive rate of less than 0.1% in our laboratory. In testing serial samples from five chimpanzees experimentally infected with hepatitis B virus, we found that hepatitis B virus DNA was detected 2-3 weeks before the appearance of hepatitis B surface antigen, and it continued to be detectable 1-3 weeks after the production of antibody to hepatitis B surface antigen. In testing serum from 84 human patients, we found hepatitis B virus DNA in all patients who had hepatitis B surface antigen and hepatitis B e antigen in serum and in 64% of the patients with hepatitis B surface antigen with antibody to hepatitis B e antigen in serum. Also, 3 out of 11 patients who were chronic hepatitis B carriers and who subsequently lost hepatitis B surface antigen were found to test positive for hepatitis B virus in serum. In contrast, all patients who lost hepatitis B surface antigen after acute hepatitis B virus infection or those classified as having non-A, non-B hepatitis tested negative for hepatitis B virus DNA. Thus, the modified PCR technique is a sensitive and rapid method for detecting hepatitis B virus DNA-containing virions in serum.

Animals↗

PubMed1995

The construction and analysis of M13 libraries prepared from YAC DNA.

Yeast artificial chromosomes (YACs) provide a powerful way to isolate and map large regions of genomic DNA and their use in genome analysis is now extensive. We modified a series of procedures to produce high quality shotgun libraries from small amounts of YAC DNA. Clones from several different libraries have been sequenced and analyzed for distribution, sequence integrity and degree of contamination from yeast DNA. We describe these procedures and analyses and show that sequencing at about 1-fold coverage, followed by database comparison (survey sequencing) offers a relatively quick method to determine the nature of previously uncharacterized cosmid or YAC clones.

Bacteriophage M13↗

PubMed2002

[Experimental techniques for ancient DNA research].

The development of modern molecular biological techniques makes it possible to study minimum DNA from ancient materials. During past decade,a lot of significant achievements on ancient DNA research have been made in many fields especially in molecular evolutionary biology. The nature of degradation and contamination of ancient DNA from ancient biological materials pose a dominating problem in ancient DNA research. Therefore,the experiments should be modified based on the modern molecular techniques and more factors should be considered when the results are analyzed. In this paper,authors review the general experimental protocols on sampling,extraction and amplification as well as authenticity of ancient DNA.

English Abstract↗

PubMed1989

The further development of a mammalian DNA alkaline unwinding bioassay with potential application to hazard identification for contaminants from environmental samples.

Recently, we have detailed a DNA alkaline unwinding assay (DAUA) that can be used to rapidly measure chemically induced strand breaks in mammalian cells (Daniel et al., 1985). In this paper we present further development of this assay, including: (1) studies on the relationship between DNA adducts and DNA strand breaks; (2) evaluation of the role of cytotoxicity in DNA strand breaks; and (3) application of the DAUA to cell preparations from the liver of mice dosed with methylating agents. The level of DNA adducts produced in human CCRF-CEM cells by treatment with benzo(a)pyrene diol-epoxide (BPDE), N-acetoxy-2-acetyl aminofluorene (AAAF), and various methylating agents was linear with concentration over several orders of magnitude. Likewise, the level of strand breaks increased with the concentration over the same dose range. The strand breaks/adduct ratio ranged from 0.05 for the methyl adducts to 0.001 for the BPDE adducts. Using these values and the inherent sensitivity of the DAUA (circa 100 to 1000 breaks/cell), (Daniel et al., 1985), the ability of the assay to detect DNA damage induced by various classes of chemical carcinogens can be calculated. The DAUA appears to be useful for assessing the relative potency of various environmental genotoxic effects on mammalian cells. In addition, it can be conducted on cells isolated from target organs of whole animals.

Animals↗

PubMed1993

Antibiotic preparations contain DNA: a source of drug resistance genes?

Fluorescence measurements and polymerase chain reaction amplification of streptomycete 16S ribosomal DNA sequences were used to show that a number of antibiotic preparations employed for human and animal use are contaminated with chromosomal DNA of the antibiotic-producing organism. The DNA contains identifiable antibiotic resistance gene sequences; the uptake of this DNA by bacteria and its functional incorporation into bacterial replicons would lead to the generation of antibiotic resistance determinants. We propose that the presence of DNA encoding drug resistance in antibiotic preparations has been a factor in the rapid development of multiple antibiotic resistance in bacteria.

Anti-Bacterial Agents↗

PubMed1998

Fixation conditions for DNA and RNA in situ hybridization: a reassessment of molecular morphology dogma.

Neutral buffered formalin (NBF) (4% neutral buffered formaldehyde) has been advocated by most investigators as the primary fixative of choice for in situ hybridization (ISH), and specific anecdotal cautions interdicting the use of precipitating fixatives, which otherwise may offer certain advantages such as superior nuclear detail, are common. Few systematic studies addressing ISH fixation conditions have been published. We reasoned that heavy metals present in some precipitating fixatives may compromise duplex formation during ISH. Cell lines containing known viral gene content (CaSki, 200 to 600 human papilloma virus 16 copies/cell, and SiHa, 1 to 2 human papilloma virus 16 copies/cell) and two negative cell lines (K562 and MOLT 4) were expanded to >10(10) and pellets fixed in NBF, zinc formalin, B5, and Bouin's and Hollande's solutions, and subjected to DNA ISH using biotinylated genomic probes. Ten tissue biopsies fixed in both Hollande's and NBF solutions were also evaluated for human papilloma virus content using DNA ISH. Additionally, 17 cases of Hodgkin's disease fixed in B5 and formalin were compared for Epstein-Barr encoded RNA detection using RNA ISH with fluorescein isothiocyanate-labeled oligonucleotides. Catalyzed reporter deposition combined with Streptavidin-Nanogold staining and silver acetate autometallography (Catalyzed reporter deposition-Ng-autometallography ISH) and a conventional indirect alkaline phosphatase method were used for detection for both DNA and RNA. Contaminating heavy metals entrapped in fixed tissues were removed by two exposures to Lugol's iodine. Results for both DNA and RNA ISH comparing B5 and NBF fixatives were virtually identical. Hollande's, Bouin's, B5, and zinc formalin fixed tissue showed results indistinguishable from NBF fixed tissue in DNA ISH. Precipitating fixatives such as B5 and Hollande's solution may be used for DNA and RNA ISH under appropriate conditions.

Cells, Cultured↗