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1.
Summary Cu/Zn Superoxide dismutase (SOD) was quantified by enzyme immunoassay for prenatal diagnosis of Down's syndrome. Overall, 154 samples of amniotic fluid, 72 samples of amniotic cells and 31 samples of chorionic tissue were investigated. Due to the large biological variance of the SOD concentrations in normal pregnancies (range for amniotic fluid 10.5–154.9, for amniotic cells 40.0–338.8, and for chorionic tissue 132.2–649.5 g SOD/g protein) the cases of Down's syndrome detected by karyotype analysis were not reliably identified by Cu/Zn SOD quantification. As in erythrocytes obtained from patients with Down's syndrome, a trisomy 21 was easily and accurately detected in the erythrocytes from very small quantities (about 50 l) of umbilical blood. The SOD concentrations in normal cases (n = 40) varied between 11.4 and 17.3 and in the cases of trisomy 21, as confirmed by karyotyping (n = 4), between 22.5 and 23.2ng/one million cells. SOD quantification in fetal erythrocyte is a helpful additional method in prenatal Down syndrome diagnosis under certain conditions, which are discussed.  相似文献   

2.
Difficulties in efficient DNA extraction from deep-sea volcanic basalt, due to high metal concentration, complex organic matter, or sometimes the low biomass, have hampered the understanding of the significant biosphere both at and below the sea floor. In order to optimize the DNA extraction from basaltic rocks, sterilized basalts with different particle sizes and chemically synthesized goethite were inoculated with an iron oxidizer Marinobacter aquaeolei and an extreme halophilic archaeon Halobaculum gomorrense respectively, and extracted with several methods. Large variations in DNA yields by different extracting methods including FastDNA® spin for soil kit, GeneClean® for ancient DNA kit, UltraClean? and traditional phenol-chloroform methods. Among the commercially available kits tested here, FAST spin kit and GeneClean® for ancient DNA kit yield 10 times more DNA than the UltraClean? kit used. In combination with FAST spin kit, skim milk greatly enhanced the archaeal DNA yields. DNA extracting efficiency was low with the cell number lower than 1 × 106 cells, but reached as high as 88% with a cell number of 1 × 108 cells. On these points, different strategies should be taken into consideration for the DNA extraction from basalts, depending on original biomass and cell types anticipated. FAST spin kit could provide high quality bacterial DNA for downstream PCR whilst the combination of FAST spin kit with skim milk would greatly enhance the archaeal DNA yields. GeneClean® for ancient DNA kit is also recommended for archaeal DNA extraction from deep sea basalt due to its high yield.  相似文献   

3.
Droplet-digital polymerase chain reaction (ddPCR) technique was set up to detect/quantify Merkel cell polyomavirus (MCPyV) DNA in clinical specimens, including chorionic villi and peripheral blood mononuclear cells (PBMCs) from spontaneous abortion (SA)-affected females. This ddPCR assay showed high accuracy, sensitivity, and specificity in detecting MCPyV DNA cloned in a recombinant plasmid vector, the control. ddPCR was extended to MCPyV DNA to investigate/quantify its sequences in clinical samples. Overall, 400 samples were analyzed, that is, 100 chorionic villi and 100 PBMCs, from SA females (n = 100), the cases, and 100 chorionic villi and 100 PBMCs from females who underwent voluntary pregnancy interruption (VI, n = 100), the control. MCPyV DNA was detected in 4/100 (4%) and 5/100 (5%) of SA and VI chorionic villi, respectively. The mean viral DNA load was 1.99 ( ± 0.94 standard mean deviation [SD]) copy/104 cells in SA and 3.02 ( ± 1.86 [SD]) copy/104 cells in VI. In PBMCs, MCPyV DNA was revealed in 9/100 (9%) and 14/100 (14%) of SA and VI, with a mean of 2.09 ( ± 1.17 [SD]) copy/104 cells and 4.09 ( ± 4.26 [SD]) copy/104 cells in SA and VI, respectively. MCPyV gene expression analysis by quantitative PCR for the large T antigen (LT) and viral capsid protein 1 (VP1) showed their mRNAs in 2/4 (50%) SA- and 2/5 (40%) VI-MCPyV-positive samples. MCPyV DNA was detected/quantified using the ddPCR technique, in chorionic villi and PBMCs from SA and VI. In our experimental conditions, ddPCR provided a powerful tool to detect/quantify MCPyV DNA sequences in clinical samples.  相似文献   

4.
Circulating tumor cells (CTC) are rare cells which have left the primary tumor to enter the blood stream. Although only a small CTC subgroup is capable of extravasating, the presence of CTCs is associated with an increased risk of metastasis and a shorter overall survival. Understanding the heterogeneous CTC biology will optimize treatment decisions and will thereby improve patient outcome. For this, robust workflows for detection and isolation of CTCs are urgently required. Here, we present a workflow to characterize CTCs by combining the advantages of both the CellSearch® and the CellCelector? micromanipulation system. CTCs were isolated from CellSearch® cartridges using the CellCelector? system and were deposited into PCR tubes for subsequent molecular analysis (whole genome amplification (WGA) and massive parallel multigene sequencing). By a CellCelector? screen we reidentified 97% of CellSearch® SKBR‐3 cells. Furthermore, we isolated 97% of CellSearch®‐proven patient CTCs using the CellCelector? system. Therein, we found an almost perfect correlation of R= 0.98 (Spearman's rho correlation, n = 20, p < 0.00001) between the CellSearch® CTC count (n = 271) and the CellCelector? detected CTCs (n = 252). Isolated CTCs were analyzed by WGA and massive parallel multigene sequencing. In total, single nucleotide polymorphisms (SNPs) could be detected in 50 genes in seven CTCs, 12 MCF‐7, and 3 T47D cells, respectively. Taken together, CTC quantification via the CellCelector? system ensures a comprehensive detection of CTCs preidentified by the CellSearch® system. Moreover, the isolation of CTCs after CellSearch® using the CellCelector? system guarantees for CTC enrichment without any contaminants enabling subsequent high throughput genomic analyses on single cell level. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:125–132, 2017  相似文献   

5.
In cartilage tissue engineering, viable cell numbers should be correctly counted in the collagenase digest of the biopsied cartilage. However, this is a difficult task due to the presence of matrix debris, cell ghosts and their aggregates. To search for the correct cell counting method in this situation, we evaluated the utility of an automatic cell counting device, the NucleoCounter, and compared it with conventional staining using the LIVE/DEAD® kit. We first measured the cell numbers of a standard chondrocyte sample by the NucleoCounter, which showed a high accuracy (R2 = 0.9999) and reproducibility (%CV: 2.00–8.66). We then calculated the cell numbers and viability in some collagenase digests of native cartilage using either the NucleoCounter or LIVE/DEAD® kit, revealing that the total cell numbers, viable ones and viability were highly correlated between them (R2 = 0.9601, 0.9638 and 0.917, respectively). However, both the intrapersonal and interpersonal variabilities in the NucleoCounter was significantly decreased to about 1/20–1/5, compared to that of the LIVE/DEAD® kit. The NucleoCounter was regarded as a useful tool for simple, rapid, and highly reproducible cell counts, which may not only provide constant experimental data in a certain laboratory, but also contribute to the high reproducibility of the clinical results of cartilage tissue engineering among multiple institutions.  相似文献   

6.
Invasive prenatal testing has become an important way to evaluate fetuses at increased risk for hereditary disorders. In utero sampling of fetal skin, liver, and muscle may be required to diagnose before-birth disorders that cannot be diagnosed by analysis using chorionic villi or amniotic fluid. In the next few years, many of these conditions will be detected by DNA analysis, and the need for these procedures may decrease dramatically. First performed by fetoscopy, fetal tissue sampling is now most frequently done by inserting a biopsy needle under continuous ultrasonographic guidance. We describe the indications, techniques, complications, and experience with obtaining fetal skin, liver, and muscle biopsy specimens.  相似文献   

7.
《Epigenetics》2013,8(11):1141-1152
Analysis of epigenetic mechanisms, particularly DNA methylation, is of increasing interest for epidemiologic studies examining disease etiology and impacts of environmental exposures. The Infinium HumanMethylation450 BeadChip® (450K), which interrogates over 480?000 CpG sites and is relatively cost effective, has become a popular tool to characterize the DNA methylome. For large-scale studies, minimizing technical variability and potential bias is paramount. The goal of this paper was to evaluate the performance of several existing and novel color channel normalizations designed to reduce technical variability and batch effects in 450K analysis from a large population study. Comparative assessment of 10 normalization procedures included the GenomeStudio® Illumina procedure, the lumi smooth quantile approach, and the newly proposed All Sample Mean Normalization (ASMN). We also examined the performance of normalizations in combination with correction for the two types of Infinium chemistry utilized on the 450K array. We observed that the performance of the GenomeStudio® normalization procedure was highly variable and dependent on the quality of the first sample analyzed in an experiment, which is used as a reference in this procedure. While the lumi normalization was able to decrease batch variability, it increased variation among technical replicates, potentially reducing biologically meaningful findings. The proposed ASMN procedure performed consistently well, both at reducing batch effects and improving replicate comparability. In summary, the ASMN procedure can improve existing color channel normalization, especially for large epidemiologic studies, and can be successfully implemented to enhance a 450K DNA methylation data pipeline.  相似文献   

8.
Mycoplasmas are the most important contaminants of cell cultures throughout the world. They are considered as a major problem in biological studies and biopharmaceutical economic issues. In this study, our aim was to find the best standard technique as a rapid method with high sensitivity, specificity and accuracy for the detection of mycoplasma contamination in the cell lines of the National Cell Bank of Iran. Thirty cell lines suspected to mycoplasma contamination were evaluated by five different techniques including microbial culture, indirect DNA DAPI staining, enzymatic mycoalert® assay, conventional PCR and real-time PCR. Five mycoplasma-contaminated cell lines were assigned as positive controls and five mycoplasma-free cell lines as negative controls. The enzymatic method was performed using the mycoalert® mycoplasma detection kit. Real-time PCR technique was conducted by PromoKine diagnostic kits. In the conventional PCR method, mycoplasma genus-specific primers were designed to analyze the sequences based on a fixed and common region on 16S ribosomal RNA with PCR product size of 425 bp. Mycoplasma contamination was observed in 60, 56.66, 53.33, 46.66 and 33.33 % of 30 different cell cultures by real-time PCR, PCR, enzymatic mycoalert®, indirect DNA DAPI staining and microbial culture methods, respectively. The analysis of the results of the different methods showed that the real-time PCR assay was superior the other methods with the sensitivity, specificity, accuracy, predictive value of positive and negative results of 100 %. These values were 94.44, 100, 96.77, 100 and 92.85 % for the conventional PCR method, respectively. Therefore, this study showed that real-time PCR and PCR assays based on the common sequences in the 16S ribosomal RNA are reliable methods with high sensitivity, specificity and accuracy for detection of mycoplasma contamination in cell cultures and other biological products.  相似文献   

9.
Harzer  K.  Schuster  I. 《Human genetics》1989,84(1):83-85
Summary Sixteen pregnancies in families with children enzymatically diagnosed as having Krabbe disease (KD) were monitored for prenatal KD using the assay of galactosyl ceramide -galactosidase (GCG) in uncultured chorionic villi (CV), cultured CV, or cultured amniotic fluid cells (AFC). Prenatal KD diagnoses were made for 5 pregnancies on the basis of lower than 10% normal GCG activity in cultured CV or AFC. Uncultured CV were studied in 3 out of the 5 KD embryos, although the GCG activities of 14%–23% as compared with control villi were diagnostically inconclusive; the relatively high activities were considered to be caused by maternal GCG contamination of these very small villus samples. Although the villi from 6 of the other pregnancies yielded more conclusive results, the use of uncultured CV alone is not recommended for prenatal KD diagnosis, this material being subject to possible uncontrolled contamination with maternal enzyme.  相似文献   

10.
A DNA extraction kit, ISOHAIR® (Nippon Gene), which was originally developed for preparing DNA from hair and nail samples, was used to prepare nematode DNA for PCR and sequencing analyses. The methods provided here, which involved digesting (resolving) a single nematode individual in a tube containing the mixed enzyme solution, enabled the DNA to be prepared within 20 min. The prepared DNA was suitable for PCR amplification of near-full-length small subunit ribosomal RNA (ca 1.7 kb), of the D2/D3 expansion segments of large subunit RNA (ca. 0.7 kb), and of partial mitochondrial COI (ca. 0.7 kb) genes, followed by sequencing analysis. Furthermore, the prepared material could be preserved in a freezer (?30 °C) for at least 20 months, and more than 300 PCR reactions could be performed from a single individual nematode.  相似文献   

11.
Epilithic bacterial community viability was assessed on natural biofilm assemblages from environmentally contrasting locations over a 17-months period to determine if it reflects environmental conditions or conditions within the biofilm assemblage. Vital state was assessed by membrane integrity using LIVE/DEAD® BacLight? staining kit. Samples were regularly collected in a large river, up and downstream of a large urban centre. Epilithic biomasses were similar between sites irrespective of the distinct water quality but varied temporarily, peaking up to 48 g AFDM m?2. Bacterial community composition assessed by 16S rDNA based PCR-DGGE significantly differed between sites. Bacterial densities (median of 2.5 × 1011 cell g AFDM?1) were stable whatever the sample origin or biomass. Viable bacterial fractions ranged between 13 and 83% of the total bacterial densities and were correlated with hydrological stability indicators (average of 41.9% during stable water periods, 62.4% during intermediate flow regimes and 50.0% during flow instability) and seasonal parameters. At the river section and epilithic community scales, consistent bacterial densities per unit of biomass could reflect a biofilm assemblage carrying capacity while variable membrane integrity likely integrates changes in the vital state of the community under changing environmental conditions.  相似文献   

12.
Mutation of hypoxanthine guanine phosphoribosyltransferase (HPRT) gives rise to Lesch-Nyhan syndrome, which is characterized by hyperuricemia, severe motor disability, and self-injurious behavior, or HPRT-related gout (Kelley-Seegmiller syndrome). The marked heterogeneity of HPRT deficiency is well known, with more than 300 mutations at the HPRT gene locus having been reported (deletions, insertions, duplications, abnormal splicing, and point mutations at different sites of the coding region from exons 1 to 9). We have identified mutations in Asian families with patients manifesting different clinical phenotypes, including rare cases of female subjects, by analyzing all nine exons of the HPRT gene (HPRT1) from genomic DNA and reverse-transcribed mRNA using the polymerase chain reaction technique coupled with direct sequencing. We developed suitable methods to detect the mutations identified from respective families with HPRT deficiency. Then, prenatal genetic diagnoses in HPRT-deficient families were carried out using both mRNA and genomic DNA from chorionic villi or amniotic fluid cells. As shown here in the heterogeneity of HPRT mutations, the spectrum of 70 mutations identified in the Asian population fits the four main conclusions that emerged previously from worldwide analysis.  相似文献   

13.
Aims: To evaluate six commercial DNA extraction kits for their ability to isolate PCR‐quality DNA from Bacillus spores in various soil samples. Methods and Results: Three soils were inoculated with various amounts of Bacillus cereus spores to simulate an outbreak or intentional release of the threat agent Bacillus anthracis. DNA was isolated from soil samples using six commercial DNA extraction kits. Extraction and purification efficiencies were assessed using a duplex real‐time PCR assay that included an internal positive control. The FastDNA® SPIN kit for Soil showed the highest DNA extraction yield, while the E.Z.N.A.® Soil DNA and PowerSoil® DNA Isolation kits showed the highest efficiencies in removing PCR inhibitors from loam soil extracts. Conclusions: The results of this study suggest that commercially available extraction kits can be used to extract PCR‐quality DNA from bacterial spores in soil. The selection of an appropriate extraction kit should depend on the characteristics of the soil sample and the intended downstream application. Significance and Impact of the Study: The results of this study aid in the selection of an appropriate DNA extraction kit for a given soil sample. Its application could expedite sample processing for real‐time PCR detection of a pathogen in soil.  相似文献   

14.
Clinical DNA is often available in limited quantities requiring whole-genome amplification for subsequent genome-wide assessment of copy-number variation (CNV) by array-CGH. In pre-implantation diagnosis and analysis of micrometastases, even merely single cells are available for analysis. However, procedures allowing high-resolution analyses of CNVs from single cells well below resolution limits of conventional cytogenetics are lacking. Here, we applied amplification products of single cells and of cell pools (5 or 10 cells) from patients with developmental delay, cancer cell lines and polar bodies to various oligo tiling array platforms with a median probe spacing as high as 65 bp. Our high-resolution analyses reveal that the low amounts of template DNA do not result in a completely unbiased whole genome amplification but that stochastic amplification artifacts, which become more obvious on array platforms with tiling path resolution, cause significant noise. We implemented a new evaluation algorithm specifically for the identification of small gains and losses in such very noisy ratio profiles. Our data suggest that when assessed with sufficiently sensitive methods high-resolution oligo-arrays allow a reliable identification of CNVs as small as 500 kb in cell pools (5 or 10 cells), and of 2.6–3.0 Mb in single cells.  相似文献   

15.
Aims: To develop a quantitative PCR assay for sensitive and specific detection of Mycobacterium avium ssp. paratuberculosis (Map) in a range of dairy products. Methods and Results: TaqMan® assays were designed to target the IS900 and f57 genetic elements of Map. Both real‐time PCR assays were integrated with the Adiapure® Map DNA extraction kit and assessed separately for the detection/quantification of Map in spiked milk, Cheddar cheese and milk powder. Assays were validated against Cheddar cheese samples containing known concentrations of Map. The IS900 qPCR assay was significantly more sensitive than the assay based on the f57 primer/probe. At a threshold cycle value of 38, limits of detection (LOD) for the IS900 qPCR assay were 0·6 CFU ml?1, 2·8 CFU g?1 and 30 CFU g?1 for artificially contaminated pasteurized milk, whole milk powder and Cheddar cheese, respectively. The respective LOD’s for the f57 assay were 6·2 CFU ml?1, 26·7 CFU g?1 and 316 CFU g?1. Conclusion: The integrated Adiapure® extraction – IS900 real time assay described is a sensitive, quantitative method for the detection of Map in dairy products. This is the first study to consider qPCR as a quantitative estimation of Map‐DNA in cheese and whole milk powder. Significance and Impact of the Study: The assay developed allows sensitive detection and quantification of Map DNA in a range of dairy products which is valuable for the screening and surveillance of this potential zoonotic organism.  相似文献   

16.
ABSTRACT: BACKGROUND: The noninvasive prenatal diagnosis procedures that are currently used to detect geneticdiseases do not achieve desirable levels of sensitivity and specificity. Recently, fetalmethylated DNA biomarkers in maternal peripheral blood have been explored for thenoninvasive prenatal detection of genetic disorders. However, such efforts have covered onlychromosomal aneuploidy, and fetal methylated DNA biomarkers in maternal whole blood fordetecting single-gene diseases remain to be discovered. METHODS: To address this issue, we systematically screened significantly hypermethylated genes in fetaltissues and compared them with maternal peripheral blood potential in an attempt to detectfetal genes in maternal peripheral blood. First, the methylated-CpG island recovery assaycombined with a CpG island array was performed for four fetus-toward placental tissues andthe corresponding maternal peripheral bloods. Subsequently, direct bisulfite sequencing andcombined bisulfite restriction analysis (COBRA) were carried out to validate the methylationstatus of the hypermethylated genes that were identified by the microarray analysis. RESULTS: Three hundred and ten significantly hypermethylated genes in the placental tissues weredetected by microarray. From the top 15 hypermethylated genes detected by microarray, twowere selected for sequencing validation in placental tissue and chorionic villus samples andfour were selected for COBRA validation in four placental tissues, ten amniotic fluids andfive chorionic villus samples. The six selected genes were confirmed to be hypermethylatedin placental tissue and chorionic villus samples, but methylation of the genes could not bedetected in the amniotic fluids. CONCLUSIONS: Of the many hypermethylated genes and methylation sites that were found in the fetal tissues,some have great potential to be developed into molecular markers for noninvasive prenataldiagnosis of monogenic disorders. Further clinical studies are warranted to confirm thesefindings.  相似文献   

17.
With climate change threatening the future of coral reefs, there is an urgent need for effective coral tissue preservation and repositories from which DNA can be extracted. Most collections use 95 % ethanol as the storage medium, but its efficacy for long-term storage for short-fragment DNA use remains poorly documented. We conducted an accelerated DNA aging trial on three species of coral to ascertain whether ethanol-stored tissue and skeleton samples could yield fit-for-purpose DNA at time scales of 100+ yrs. We conclude that even using a crude DNA extraction technique, samples kept at 40 °C for 20 months yielded DNA of sufficient quality for Symbiodinium and coral host genotyping. If stored at ?20 °C, these samples are likely to still yield useable DNA after 100 yrs. Ethanol-stored samples compared favorably in terms of DNA quality, quantity and sample integrity with those stored in an analogue of the commercial storage buffer RNAlater ®.  相似文献   

18.
DNA was efficiently and quantitatively isolated from extremely small quantities of mycelia (0.1–10 mg) of different phytopathogenic moulds by grinding freeze-dried mycelia with glass beads and then using a commercial DNA extraction kit. The efficiency of disruption of the mycelia and the quantitative DNA extraction was proved by microscopy and the quantification of isolated DNA by real time PCR. Presented at the 27th Mykotoxin-Workshop, Dortmund, Germany, June 13–15, 2005 Financial support: German Research Foundation (DFG grant Pr 708/2). J.M. thanks the Cusanuswerk for a doctoral scholarship  相似文献   

19.
A photo-Fenton-membrane bioreactor (MBR) coupled system is an innovative tool for the treatment of wastewater containing high quantities of contaminants. In this paper, wastewater with 200 mg l?1 of dissolved organic carbon (DOC) of a selected mixture of five commercial pesticides: Vydate®, Metomur®, Couraze®, Ditimur-40®, and Scala® was treated by combining photo-Fenton and MBR. The effect of photo-treated pollutants on MBR operation was investigated by studying the population changes that occurred with time in the activated sludge of the biological system. Pre-treatment with photo-Fenton was carried out (only up to 34% of mineralization of DOC) and, after MBR treatment, 98% of biodegradation efficiency was obtained. During the biological treatment, little changes in the activated sludge population were detected by DGGE analysis, maintaining acceptable biodegradation efficiency, which points out the robustness of the MBR treatment versus changes in feed composition.  相似文献   

20.
Aneuploidies involving chromosomes 21, 18, 13, X and Y account for over 95% of all chromosomal abnormalities in live-born infants. Prenatal diagnosis of these disorders is usually accomplished by cytogenetic analysis of amniotic or chorionic cells but this is a lengthy procedure requiring great technical expertise.In this paper, we assess the diagnostic value of using a quantitative fluorescent polymerase chain reaction (PCR) suitable for the simultaneous and rapid diagnosis of trisomies 21 and 18 together with the detection of DNA sequences derived from the X and Y chromosomes. Samples of DNA, extracted from amniotic fluid, fetal blood or tissues, and peripheral blood from normal adults were investigated by quantitative fluorescent PCR amplification of polymorphic small tandem repeats (STRs) specific for two loci on each of chromosomes 21 and 18. Quantitative analysis of the amplification products allowed the diagnosis of trisomies 21 and 18, while sexing was performed simultaneously using PCR amplification of DNA sequences derived from the chromosomes X and Y. These results indicate the advantages of using two sets of STR markers for the detection of chromosome 21 trisomies and confirmed the usefulness of quantitative fluorescent multiplex PCR for the rapid prenatal diagnosis of selected chromosomal abnormalities. Received: 23 January 1996 / Revised: 21 February 1996  相似文献   

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