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PubMed1993

Applicability of DNA isolated from syncytiotrophoblast vesicles to gene amplification and molecular analysis.

Maternal contamination of fetal DNA represents a major problem when highly sensitive molecular techniques are used in the prenatal diagnosis of genetic diseases. For this reason, we have studied the possibility of using DNA isolated from syncytiotrophoblast vesicles as a target of gene amplification (PCR). Three PCR systems were selected which included a repetitive 149 bp fragment of the Y chromosome, the VNTR locus D1S80, and a portion of the beta-globin gene. The results of these experiments indicate that DNA isolated from syncytiotrophoblast vesicles is free of maternal contamination and is suitable for gene amplification and DNA analysis.

DNA↗
PubMed2003

Safety assessment of Bt 176 maize in broiler nutrition: degradation of maize-DNA and its metabolic fate.

Insect resistant Bt 176 maize has been developed by genetic modification to resist European borer infection. In the present investigation, the experiment was conducted to determine the effect of feeding a new hybrid of Bt 176 maize (NX 6262- Bt 176) on general health condition and performance of broiler chickens. Maize grains and diets were subjected to proximate analysis. Amino and fatty acids investigation were applied for both maize grains before used. To evaluate the degradation of NX 6262- Bt 176 maize DNA and its metabolic fate in broiler blood, muscles and organs. One-day-old male broilers were fed ad libitum on either an experimental diet containing NX 6262- Bt 176 or a control diet containing the non-modified maize grains for 35 days. Feed consumption and body weight were recorded weekly during the experimental period. All chickens were subjected to nutritional evaluation period at day 20 of age for 5 successive days, to calculate the percentage of apparent digestible nutrients in both diets. At day 35 samples were collected at several intervals after feed withdrawal. Prior to slaughter blood samples were collected from all birds by heart puncture to prevent DNA cross contamination. Samples from pectoral and thigh muscles, liver, spleen, kidney, heart muscle, bursa and thymus glands were collected. Digesta from different sections of the gastrointestinal tract (GIT) were collected as well. Packed cell volume (PCV) and some serum parameters were investigated. There were no significant differences between control and experimental group concerning chemical composition of feeds, apparent digestible nutrients, and all performance parameters measured (P > 0.05). Furthermore, there were no differences in the PCV and the analysed serum parameters between the control and experimental group. The results of maize DNA digestibility showed that the new variety takes the normal physiological passage along broiler GIT similar to the conventional line. In addition, Bt 176 maize DNA appears to be partially degraded in different parts of GIT comparable to the DNA of the control maize line. Results of the metabolic fate of maize DNA in broiler blood, muscles and organs indicated that only short DNA fragments (199 bp) derived from the plant chloroplast gene could be detected in the blood, skeletal muscles, liver, spleen and kidney, which disappeared after prolongation the fasting time. In heart muscle, bursa of Fabricius and thymus, no plant chloroplast DNA was found. Bt gene specific constructs from Bt 176 maize were not detected in any investigated blood or tissue samples.

Animal Feed↗
PubMed1991

Detection of interferon-gamma mRNA in psoriatic epidermis by polymerase chain reaction.

Psoriatic skin lesions contain HLA-DR positive T lymphocytes, and other activation antigens, which suggest that the T cells may be producing lymphokines. Gamma interferon is produced by activated T cells, and its presence in psoriasis has been inferred by the lesional keratinocyte expression of 3 gamma interferon-inducible proteins i.e. HLA-DR, intercellular adhesion molecule-1, and gamma-IP-10. To determine whether gamma interferon is being produced directly in psoriatic lesions, punch biopsies of normal and diseased skin were separated into epidermal sheets and dermal fragments. Total cellular RNA was isolated from each epidermal and dermal compartment, and reverse transcribed followed by amplification of the resultant DNA by polymerase chain reaction. The amplification process involved the use of 5' and 3' primers for gamma interferon, and tumor necrosis factor-alpha, with beta-actin serving as a control. Gamma interferon mRNA, but not tumor necrosis factor alpha mRNA, was detectable in 4 of 5 psoriatic epidermal specimens. Neither mRNA was detectable in any normal skin dermal/epidermal specimens. Gamma interferon mRNA was also detectable in a single psoriatic dermal specimen. If reverse transcriptase was omitted, no polymerase chain reaction products were detected, indicating that the fragments detected were not derived from contaminating genomic DNA. These results indicate that gamma interferon mRNA can be extracted and successfully detected from human psoriatic lesional skin biopsies, using polymerase chain reaction technology. This molecular approach can easily be expanded to measure many other cytokines in both epidermal and dermal locations. The detection of gamma interferon in this clinical setting may be of particular pathophysiological significance because injection of gamma interferon has been reported to induce psoriatic lesions.

Actins↗
PubMed1986

DNA-diagnosis of sickle cell anemia from chorionic villi: possible influence of maternal cell contamination.

The admixture of maternal tissue is a possible hazard of prenatal diagnosis from chorionic villi. Therefore the tolerable degree of maternal DNA contamination in prenatal diagnosis of sickle cell anemia was investigated by mixing various amounts of DNA from HbS carriers with DNA from normal individuals and sickle cell anemia patients. The results indicate that lower rate of admixed maternal DNA does not prevent an exact direct DNA-diagnosis of sickle cell anemia.

Anemia, Sickle Cell↗
PubMed2002

Improved detection of endoparasite DNA in soil sample PCR by the use of anti-inhibitory substances.

Although there have been numerous microbial examinations of soil for the presence of human pathogenic developmental parasite stages of Ancylostoma caninum and Toxocara canis, molecular techniques (e.g. DNA extraction, purification and subsequent PCR) have scarcely been applied. Here, DNA preparations of soil samples artificially contaminated with genomic DNA or parasite eggs were examined by PCR. A. caninum and T. canis-specific primers based on the ITS-2 sequence were used for amplification. After the sheer DNA preparation a high content of PCR-interfering substances was still detectable. Subsequently, two different inhibitors of PCR-interfering agents (GeneReleaser, Bioventures Inc. and Maximator, Connex GmbH) were compared in PCR. Both substances increased PCR sensitivity greatly. However, comparison of the increase in sensitivity achieved with the two compounds demonstrated the superiority of Maximator, which enhanced sensitivity to the point of permitting positive detection of a single A. caninum egg and three T. canis eggs in a soil sample. This degree of sensitivity could not be achieved with GeneReleaser for either parasite Furthermore, Maximator not only increased sensitivity; it also cost less, required less time and had a lower risk of contamination. Future applications of molecular methods in epidemiological examinations of soil samples are discussed/elaborated.

Ancylostoma↗
PubMed1995

PCR strategy for identification and differentiation of small pox and other orthopoxviruses.

Rapid identification and differentiation of orthopoxviruses by PCR were achieved with primers based on genome sequences encoding the hemagglutinin (HA) protein, an infected-cell membrane antigen that distinguishes orthopoxviruses from other poxvirus genera. The initial identification step used a primer pair of consensus sequences for amplifying an HA DNA fragment from the three known North American orthopoxviruses (raccoonpox, skunkpox, and volepox viruses), and a second pair for amplifying virtually the entire HA open reading frame of the Eurasian-African orthopoxviruses (variola, vaccinia, cowpox, monkeypox, camelpox, ectromelia, and gerbilpox viruses). RsaI digest electropherograms of the amplified DNAs of the former subgroup provided species differentiation, and TaqI digests differentiated the Eurasian-African orthopoxviruses, including vaccinia virus from the vaccinia virus subspecies buffalopox virus. Endonuclease HhaI digest patterns distinguished smallpox variola major viruses from alastrim variola minor viruses. For the Eurasian-African orthopoxviruses, a confirmatory step that used a set of higher-sequence-homology primers was developed to provide sensitivity to discern individual virus HA DNAs from cross-contaminated orthopoxvirus DNA samples; TaqI and HhaI digestions of the individual amplified HA DNAs confirmed virus identity. Finally, a set of primers and modified PCR conditions were developed on the basis of base sequence differences within the HA genes of the 10 species, which enabled production of a single DNA fragment of a particular size that indicated the specific species.

Animals↗
PubMed2002

High sensitivity of detection of TP53 somatic mutations by fluorescence-assisted mismatch analysis.

We analyzed exons 5-9 of the TP53 gene in 41 breast cancers using direct sequencing, PCR-SSCP (single-strand conformation polymorphism), and fluorescence-assisted mismatch analysis (FAMA), to test the level of specificity and sensitivity of each method. A major issue for the correct detection of TP53 somatic mutations in primary tumors is often represented by the large amount of normal DNA, which can cause excessive dilution of the mutant allele, with consequent possible false-negative results. High sensitivity upon dilution of the mutant allele has been demonstrated for FAMA, a method based on the chemical cleavage of a mismatch within heteroduplex DNA molecules. Exons 5-9 of the TP53 gene were analyzed by FAMA using only two long bifluorescent fragments. Differences in sensitivity, accuracy, and specificity were observed among the above-mentioned procedures. Thirteen of the 41 samples (31.7%) revealed TP53 genetic alterations by automated sequencing, 19 samples (46.3%) were positive for SSCP, whereas 14 samples (34%) showed variants detectable by FAMA. Seven samples were positive in SSCP, but negative in both FAMA and sequencing assays; however, 2 SSCP-negative samples revealed evident signals by FAMA, indicating the presence of TP53 mutations. One of the latter samples showed the alteration by sequence analysis, whereas the other failed to reveal the mutation signal even by sequencing, as a consequence of the very small amount of the mutant allele resulting from the excess of contaminating normal DNA. Our results show that FAMA may represent a suitable and accurate assay for the routine diagnosis of TP53 somatic mutations in DNAs from solid tumor biopsies.

Base Pair Mismatch↗
PubMed1977

Detection of a contaminant cell culture line by restriction endonuclease cleavage patterns of mitochondrial DNA.

A putative HeLa cell culture line was discovered to be contaminated with mouse cells by examination of agarose gel profiles of restriction endonuclease digests of mitochondrial DNA. The contamination was confirmed by karyotypic analysis, and by observation of the mouse satellite band in an analytical buoyant density centrifugation of total cellular DNA. Restriction endonuclease analysis of mitochondrial DNA is suggested as a useful method for monitoring the species of cells in culture.

Animals↗
PubMed2004

Working Group report 4: exposure assessment for biological agents.

This Working Group was assembled to review and evaluate methods currently used to estimate work site exposures to biological agents and to present recommendations on suitable measurement strategies. The current state of exposure assessment was evaluated for environments with organic dust including agriculture, composting, sewage and waste treatment processing, peat moss harvesting and handling, cotton and textile processing, greenhouse work, and grass seed processing. Methods for measurement of microbial contaminants in indoor environments were also considered. Important methods are emerging that use quantitative PCR for assessment of microbial agents. Difficulties exist with optimization of extraction to yield contaminant-free DNA without significant DNA loss. Advances in assays for microbial agents (e.g., endotoxin and glucans) as well as allergens have increased the utility of exposure assessment for these agents. A crucial area for further development is international harmonization of methodologies to reduce interlaboratory variability and to facilitate establishment of exposure guidelines. Endotoxin exposure assessment using the Limulus amebocyte lysate method is a high priority for harmonization because of its importance as a pulmonary inflammatory agent in many occupational settings.

Air Pollution, Indoor↗
PubMed1994

Inhibition, tissue distribution and hormonal specificity of a promoter-binding factor for the uteroglobin gene.

We had earlier reported a uteroglobin promoter-binding factor in nuclei from progesterone-stimulated rabbit endometrium that was inhibited by a factor in nuclei without progesterone stimulation or from non-target tissues (Rider, V., and Bullock, D.W., 1988. Biochem. Biophys. Res. Comm. 156, 1368-1375). In the course of purification of the inhibitory activity, the effect was shown to be due to contaminating genomic DNA. The inhibitor was destroyed by treatment with DNase I and resisted phenol-chloroform extraction. Fractionation of nuclear extracts on columns of DEAE-Sepharose separated the inhibitor and revealed the presence of binding activity in unstimulated or estrogen-treated endometrium, as well as in liver, lung and ovary. The tissue and hormonal specificity of the promoter binding factor is thus less restricted than recently reported.

Animals↗
PubMed2003

Construction of a deep coverage BAC library from Capsicum annuum, 'CM334'.

A bacterial artificial chromosome (BAC) library consisting of 235,000 clones with an average insert size of 130 kb was constructed from Capsicum annuum, 'CM334'. Based on a pepper haploid genome size of 2,702 Mbp/C, the BAC library is estimated to contain approximately 12 genome equivalents and represents at least 99% of the pepper genome. Screening of the library with mitochondrial DNA probes (coxII, coxIII, atp6 and atp9) and chloroplast DNA probes (atpB, rbcL) indicated that contamination with cytoplasmic DNA was less than 0.5%. To estimate the possibility of isolating a specific clone, the library was screened with single or low-copy gene-specific probes and RFLP probes. Screening of high density BAC filters with RFLP markers linked to L (TMV resistance), y (fruit color), C2 (fruit color) and C (pungency) loci under high stringency conditions revealed that at least three positive BAC clones were found per each probe. This fact indicates that the library is highly reliable and represents a resource for map-based cloning, physical mapping, and characterization of upstream and downstream regulations of the chili pepper genes.

Capsicum↗
PubMed2005

Characterization of the novel HCH-degrading strain, Microbacterium sp. ITRC1.

A gram-positive Microbacterium sp. strain, ITRC1, that was able to degrade the persistent and toxic hexachlorocyclohexane (HCH) isomers was isolated and characterized. The ITRC1 strain has the capacity to degrade all four major isomers of HCH present in both liquid cultures and aged contaminated soil. DNA fragments corresponding to the two initial genes involved in gamma-HCH degradative pathway, encoding enzymes for gamma-pentachlorocyclohexene hydrolytic dehalogenase (linB) and a 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase (linC), were amplified by PCR and sequenced. Their presence in the ITRC1 genomic DNA was also confirmed by Southern hybridization. Sequencing of the amplified DNA fragment revealed that the two genes present in the ITRC1 strain were homologous to those present in Sphingomonas paucimobilis UT26. Both 16S rRNA sequencing and phylogenetic analysis resulted in the identification of the bacteria as a Microbacterium sp. We assume that these HCH-degrading bacteria evolved independently but possessed genes similar to S. paucimobilis UT26. The reported results indicate that catabolic genes for gamma-HCH degradation are highly conserved in diverse genera of bacteria, including the gram-positive groups, occurring in various environmental conditions.

Actinomycetales↗
PubMed1990

RNA template-specific polymerase chain reaction (RS-PCR): a novel strategy to reduce dramatically false positives.

We report a novel modification of the reverse transcription-polymerase chain reaction method that we have dubbed RNA template-specific PCR (RS-PCR). With this approach, the 5' end of the first strand is tagged with a unique nucleotide sequence during reverse transcription which may then be exploited to amplify preferentially RNA-derived sequences. In our hands, RS-PCR greatly reduces the frequency of false positives and virtually eliminates carryover contamination from DNA fragments amplified in previous experiments.

Animals↗
PubMed1982

Age changes of the isoelectric points of non-histone chromosomal proteins from rat liver in the pH range 5 to 8.

Non-histone chromosomal proteins were extracted from purified nuclei of young (2-3 months) and old (24-28 months) rat liver by a two-phase partition method (chloroform:-isoamyl alcohol, 24:1) after histone depletion with 0.25N HCl. The proteins were subjected to analytical isoelectric focusing in the pH range 5-8. On the densitograms derived from Coomasie brilliant blue R-250 stained gels, there were formally four areas separated having the following pH ranges: I) 5.80-6.10; II) 6.25-6.42; III) 6.80-7.00; IV) 7.20-7.35 for young rats, and I) absent; II) 6.35-6.75; III) 6.80-7.00; IV) 7.12-7.40 for old rats. Hence, the main result is the absence of a group of proteins from old rats having the pH range 5.80-6.10. The factors involved in protein separation by isoelectric focusing, like time-dependent post-translational charge modifications: phosphorylation, acetylation, ADP-ribosylation, deamidation, terminal peptide cleavage, glycosylation, and DNA-like contaminants are discussed.

Aging↗
PubMed2006

Contribution of microdissection for the detection of microsatellite instability in colorectal cancer.

The determination ofmicrosatellite instability (MSI) is an important step in the identification of familial colorectal cancer such as hereditary nonpolyposis colon cancer. It could also be of interest in the therapeutic management of sporadic cancer. International criteria for the determination of MSI have been published, recommending the use of microdissection. The aim of this work was to evaluate the impact of contaminant normal DNA in tumor samples for MSI assessment in colorectal cancer using a microdissection technique. We performed a comparative analysis of the microsatellite status between total DNA (DNA extracted from whole tumor samples) and microdissected DNA in 3 different regions from 23 cases of colorectal cancer. Six microsatellites were amplified using fluorescent polymerase chain reaction. We analyzed 9 cases with MSI and 14 cases without instability, with similar results between total DNA and microdissected DNA. Moreover, within a same tumor, the MSI phenotype was observed regardless of the region analyzed. Thus, this work shows the reproducibility of the MSI phenotype throughout a tumor. However, we observed a regional heterogeneity of the MSI profile, consisting of variations in the number and the size of unstable alleles within different regions. This result reflects the genetic heterogeneity of colorectal cancer with MSI. In the 14 cases without instability, we observed an increase of more than 60% in the loss of heterozygosity detection rate after microdissection. Thus, this work confirms the contribution of microdissection for loss of heterozygosity assessment.

Adenocarcinoma↗
PubMed2026

Towards a Robust cell-free DNA Isolation Protocol for NGS Applications in a Clinical Molecular Diagnostics Setting.

Cell-free DNA (cfDNA), released from apoptotic and necrotic cells into body fluids, is a non-invasive source of genetic information for disease prediction, diagnosis, and monitoring. However, its low abundance makes cfDNA highly susceptible to various pre-analytical influences, potentially increasing high molecular weight (HMW) or genomic DNA (gDNA) compromising downstream cfDNA analyses. This study evaluated the impact of different cfDNA-stabilizing blood collection tubes (BCT; Cell-Free DNA BCT, Streck; S-Monovette cfDNA Exact, Sarstedt) stored at room temperature for 1, 5, or 10 days, prior to plasma isolation using different isolation methods (magnetic bead-based or silica column-based) on cfDNA stability and yield. DNA quantity and quality were assessed by fluorometric quantification, automated fragment analysis, and gene-specific quantitative PCR. Streck-based workflows maintained stable cfDNA yields and characteristic mononucleosomal fragmentation profiles across all storage times. In contrast, Sarstedt tubes showed reduced cfDNA concentrations after 5 days and a pronounced increase at 10 Days, accompanied by high-molecular weight DNA patterns consistent with white-blood cells (WBC) lysis. These trends were largely independent of the extraction method. Overall, the results demonstrate that blood collection tube chemistry critically influences cfDNA integrity during delayed processing. Streck tubes, particularly when combined with silica column-based isolation method, provided the most robust and reproducible workflow for routine molecular diagnostics, whereas Sarstedt tubes produced physiologically implausible results after extended storage.

blood collection tubes↗
PubMed2001

Development of a strand-specific RT-PCR based assay to detect the replicative form of hepatitis C virus RNA.

The recent development of tagged RT-PCR and rTth RT-PCR has greatly improved strand-specific detection of hepatitis C virus (HCV) RNA but these assays are still prone to some false detection of the incorrect strand of RNA. In this study we aimed to address additional factors which contribute towards false detection of HCV RNA. Firstly the benefits of both tagged primers and the thermostable reverse transcriptase rTth during cDNA synthesis were combined and it was found that strand specificity was greatly improved without compromising sensitivity. The reliability of the assay was then optimised by addressing the following issues: control synthetic transcripts should be free of contaminating plasmid DNA, residual RT activity should be minimised in the presence of PCR primers and cDNA should be free of unincorporated tagged RT primer prior to PCR amplification. The alterations made to the assay eliminated completely false detection of the incorrect strand of RNA in the control assay whilst the correct strand was consistently detected at a cDNA dilution of 10(-3)-10(-4). Negative strand was not detected in RNA isolated from serum but was detected, at a ten-fold lower level than positive strand, in RNA isolated from liver tissue.

DNA Repair Enzymes↗