Single-cell sequencing and mini-sequencing for preimplantation genetic diagnosis

There is increasing interest in the use of preimplantation genetic diagnosis (PGD) as an alternative to routine prenatal diagnosis. However, the costs associated with development and testing of new PGD protocols have forced some PGD centres to limit the number of diseases for which PGD is offered. One of the main factors in the design of new protocols, which affects cost and accuracy, is the choice of the mutation-detection technique. We have assessed the reliability of DNA sequencing and mini-sequencing for clinical diagnosis at the single-cell level and have found them to be rapid and accurate. Extensive optimisation for individual mutations is not usually necessary when employing these versatile techniques and consequently a smaller investment of time and resources should be required during development of new protocols. Additionally, we report single-cell protocols for the diagnoses of cystic fibrosis, sickle cell anaemia and β-thalassaemia, which utilise mini-sequencing. Unlike most mutation-detection techniques, mini-sequencing permits analysis of very small DNA fragments. Small amplicons experience low allele dropout (ADO) rates, and consequently this approach could potentially improve the reliability of PGD. Copyright © 2003 John Wiley & Sons, Ltd.     

Real-time PCR with molecular beacons provides a highly accurate assay for detection of Tay-Sachs alleles in single cells

The results presented here provide the first single-cell genetic assay for Tay-Sachs disease based on real-time PCR. Individual lymphoblasts were lysed with an optimized lysis buffer and assayed using one pair of primers that amplifies both the wild type and 1278 + TATC Tay-Sachs alleles. The resulting amplicons were detected in real time with two molecular beacons each with a different colored fluorochrome. The kinetics of amplicon accumulation generate objective criteria by which to evaluate the validity of each reaction. The assay had an overall utility of 95%, based on the detection of at least one signal in 235 of the 248 attempted tests and an efficiency of 97%, as 7 of the 235 samples were excluded from further analysis for objective quantitative reasons. The accuracy of the assay was 99.1%, because 228 of 230 samples gave signals consistent with the genotype of the cells. Only two of the 135 heterozygous samples were allele drop-outs, a rate far lower than previously reported for single-cell Tay-Sachs assays using conventional methods of PCR. Copyright © 2002 John Wiley & Sons, Ltd.     

生物强化膜生物反应器(MBR)处理邻苯二甲酸二乙酯(DEP)效果及微生物群落结构分析

为强化邻苯二甲酸二乙酯(DEP)降解,将从活性污泥中分离的高效DEP降解菌Arthrobacter sp.LMS13运用到MBR反应器,考察强化系统对DEP去除效果,并通过实时荧光定量(q-PCR)和Illumina Mi Seq技术分别对系统运行期间邻苯二甲酸双加氧酶降解基因(phtA)数量以及微生物群落结构特征进行了分析.结果表明,强化系统能加快反应器启动,对进水浓度为800 mg·L-1的DEP,强化系统和未经强化系统在运行后期(61 d)对DEP平均去除率分别为81%和19%.q-PCR结果显示,在驯化阶段,phtA基因拷贝数上升,但当DEP浓度大于400 mg·L-1时,phtA基因数量下降;phtA基因拷贝数与DEP降解率呈正相关.Mi Seq测序结果进一步表明,高浓度DEP导致系统中群落多样性指数下降,但对强化系统多样性影响相对较小.反应器运行过程中,原活性污泥中占有较高比例的拟杆菌门(Bateroidetes)和厚壁菌门(Firmicutes)丰度降低,ε-变形纲(ε-Proteobacteria)、绿弯菌门(Chloroflexi)在反应系统中逐渐被淘汰,而β-变形纲(β-Proteobacteria)和放线菌门(Actinobacteria)成为系统中的优势菌门,其中红环菌属(Rhodocyclus)、博得氏杆菌属(Bordetella)、节杆菌属(Arthrobacter)为优势菌属,在DEP降解系统中起着主要作用,是保证DEP生物处理效果和维持反应器稳定运行的重要菌属.     

Responses of activities, abundances and community structures of soil denitrifiers to short-term mercury stress

The responses of activities, abundances and community structures of soil denitrifiers to mercury (Hg) stress were investigated through a short-term incubation experiment. Four soil treatments with different concentrations of Hg (CK, Hg25, Hg50, and Hg100, denoted as 0, 25, 50, and 100 mg Hg/kg dry soil, respectively) were incubated for 28 days. Soil denitrification enzyme activity (DEA) was measured at day 3, 7 and 28. The abundances and community structures of two denitrification concerning genes, nirS (cd₁-nitrite reductase gene) and nosZ (nitrous oxide reductase gene), were analyzed using real-time PCR and denaturing gradient gel electrophoresis (DGGE). Results showed that soil DEA was significantly stimulated in the treatments of Hg25 and Hg50 compared with others at day 7. Meanwhile, no difference in the abundances of soil nirS and nosZ was found between Hg spiked treatments and CK, except the lower abundance of nirS (P<0.05) in the Hg added treatments compared with that in the CK at day 28. The community structures of denitrifiers based on nirS gene presented obvious change at day 7 along with the Hg additions, however, no variation was found in all treatments based on the nosZ gene. The results indicated that Hg (Hg25 and Hg50) had a strongly short-term stimulation on soil DEA, and nirS gene is more sensitive than nosZ gene to Hg stress.     

Quantification of microcystin-producing and non-microcystin producing Microcystis populations during the 2009 and 2010 blooms in Lake Taihu using quantitative real-time PCR

Lake Taihu, a large, shallow hypertrophic freshwater lake in eastern China, has experienced lake-wide toxic cyanobacterial blooms annually during summer season in the past decades. Spatial changes in the abundance of hepatotoxin microcystin-producing and non-microcystin producing Microcystis populations were investigated in the lake in August of 2009 and 2010. To monitor the densities of the total Microcystis population and the potential microcystin-producing subpopulation, we used a quantitative real-time PCR assay targeting the phycocyanin intergenic spacer (PC-IGS) and the microcystin synthetase gene (mcyD), respectively. On the basis of quantification by real-time PCR analysis, the abundance of potential toxic Microcystis genotypes and the ratio of the mcyD subpopulation to the total Microcystis varied significantly, from 4.08× 10⁴ to 5.22× 10⁷ copies/mL, from 5.7% to 65.8%, respectively. Correlation analysis showed a strong positive relationship between chlorophyll-a, toxic Microcystis and total Microcystis; the abundance of toxic Microcystis correlated positively with total phosphorus and ortho-phosphate concentrations, but negatively with TN:TP ratio and nitrate concentrations. Meanwhile the proportion of potential toxic genotypes within Microcystis population showed positive correlation with total phosphorus and ortho-phosphate concentrations. Our data suggest that increased phosphorus loading may be a significant factor promoting the occurrence of toxic Microcystis bloom in Lake Taihu.     

PCR-酶切技术在石油烃降解菌筛选鉴定中的应用

将以原油驯化所得的纯培养微生物菌株作为模板,采用PCR(聚合酶链式反应)法,用扩增细菌16S rDNA的一对通用引物(8 f,1492 r)对模板扩增,并用限制性内切酶R saI和M spI对PCR产物进行ARDRA多态性分析。聚类去除重复菌株后60株菌株可分为11种不同分类操作单元(OTU),同时得出每个分类操作单元的数量。实验结果表明,此方法可快速去除重复菌株并反映出菌株间的系统进化关系;同时实验数据可构建成库,使后续分离菌株的筛选工作只需比对数据即可完成。     

Analysis of the effects diclofenac has on Japanese medaka (Oryzias latipes) using real-time PCR

The expression levels of cytochrome P450 1A, p53 and vitellogenin were investigated in three different tissues of male medaka fish after exposure to diclofenac that is one of the main concerns among pharmaceuticals frequently found in sewage treatment plant (STP) effluents. The results showed that cytochrome P450 1A, p53 and vitellogenin were highly expressed in tissue-specific gene expression patterns after exposure to 8 mg/l and 1 μg/l of diclofenac. These elevated expression levels of three biomarkers suggested that diclofenac has potential to cause cellular toxicity, p53-related genotoxicity and estrogenic effects. It is also noteworthy that diclofenac has the potential to cause these effects even at an environmentally relevant concentration of diclofenac, 1 μg/l.