Duplex PCR for preimplantation genetic diagnosis (PGD) of spinal muscular atrophy

The main difficulty in developing a molecular diagnosis of spinal muscular atrophy (SMA) resides in the specific genomic structure of the locus. Indeed, two highly homologous survival motor neurone genes, SMN1 and SMN2, are present at the locus. The detection of the homozygous deletion of exons 7 and 8 of the SMN1 gene, which is present in 90 to 98% of the patients, is based on methods highlighting 1 of the 8 nucleotidic mismatches existing between these 2 genes. In order to offer preimplantation genetic diagnosis (PGD) for SMA, we developed a new allele-specific amplification method. The main disadvantage of our previously described strategy resided in the possibility of diagnosing, in case of amplification failure, an unaffected embryo as affected. We present here a new PGD-SMA method. We established the conditions for three different duplex PCRs, allowing the specific detection of the SMN1 gene and one polymorphic marker, either D5S629, D5S1977, or D5S641. Of the 60 to 90 single cells tested, the PCR efficiency varied from 98 to 100% with a complete genotype obtained in a range between 81 and 87% with a global allele drop-out rate of 9%. Such a test was used to perform 1 PGD cycle for which 7 embryos could be analysed. All the embryos were fully diagnosed, six as unaffected and one as affected. Four embryos were transferred, but no pregnancy ensued. Copyright © 2003 John Wiley & Sons, Ltd.     

亚硝态氮胁迫下菲律宾蛤仔实时定量P CR内参基因的筛选

为了更好地从基因角度研究亚硝态氮对贝类的生态毒性,需要筛选一个合适的内参基因作为参考,对其毒性相关基因进行定量表达分析。本研究以菲律宾蛤仔(Ruditapes philippinarum)作为研究对象,以亚硝态氮胁迫的鳃组织cDNA作为模板,利用geNorm软件和NormFinder软件对6个候选内参基因进行表达稳定性分析,并对2个结果做了综合赋权分析。结果显示,geNorm分析的基因表达稳定性结果为ActinCyPAEF1αUbi18STubu,NormFinder软件分析的结果为ActinUbiCyPAEF1α18STubu,最后经加权赋值法综合分析获得6个候选基因的表达稳定性为ActinCyPAUbiEF1α18STubu,即Actin为表达最稳定的基因。因此,Actin可以作为衡量亚硝态氮胁迫后菲律宾蛤仔鳃组织中基因表达的内参基因。     

A hybrid method for inverse characterization of subsurface contaminant flux

The methods presented in this work provide a potential tool for characterizing contaminant source zones in terms of mass flux. The problem was conceptualized by considering contaminant transport through a vertical "flux plane" located between a source zone and a downgradient region where contaminant concentrations were measured. The goal was to develop a robust method capable of providing a statement of the magnitude and uncertainty associated with estimated contaminant mass flux values. In order to estimate the magnitude and transverse spatial distribution of mass flux through a plane, the problem was considered in an optimization framework. Two numerical optimization techniques were applied, simulated annealing (SA) and minimum relative entropy (MRE). The capabilities of the flux plane model and the numerical solution techniques were evaluated using data from a numerically generated test problem and a nonreactive tracer experiment performed in a three-dimensional aquifer model. Results demonstrate that SA is more robust and converges more quickly than MRE. However, SA is not capable of providing an estimate of the uncertainty associated with the simulated flux values. In contrast, MRE is not as robust as SA, but once in the neighborhood of the optimal solution, it is quite effective as a tool for inferring mass flux probability density functions, expected flux values, and confidence limits. A hybrid (SA-MRE) solution technique was developed in order to take advantage of the robust solution capabilities of SA and the uncertainty estimation capabilities of MRE. The coupled technique provided probability density functions and confidence intervals that would not have been available from an independent SA algorithm and they were obtained more efficiently than if provided by an independent MRE algorithm.     

生物强化系统微生物分子诊断技术的应用及新发展

现代分子生物技术的飞速发展及其在环境研究领域的应用，为生物强化技术的研究和发展提供了新方法和新思路。本文从生物强化系统特异微生物检测及定量化技术、生物强化系统微生物群落结构组成及动态演替规律研究、生物强化作用机制的分子生物学解析、生物强化菌的基因工程构建、生物强化系统微生物的安全释放及控制技术几方面，对生物强化系统微生物分子诊断技术的应用和发展作了较为全面的综述。     

火山岩填料曝气生物滤池的SNAD工艺启动特性及功能菌丰度演替

为研究同步亚硝化、厌氧氨氧化耦合反硝化(SNAD)工艺在浸没式生物滤池反应器(SBAF)内的运行特性,同时接种亚硝化污泥和富集ANAMMOX的填料启动SNAD反应器.结果表明在60 mg·L~(-1)有机物浓度下,自养脱氮和反硝化实现较好的耦合,并在该浓度下稳定运行了67 d,其总氮去除率最高可达92.0%,COD去除率最高达82.9%,最高总氮去除负荷为2.3 kg·(m~3·d)~(-1).与全程自养脱氮(CANON)工艺相比,SNAD工艺的平均总氮去除率提高了12.6%.荧光定量PCR结果显示,系统启动后AOB菌的丰度有所增长,ANAMMOX菌的丰度增长了1个数量级,而NOB菌和反硝化菌的数量维持在较低水平(小于10~7 copies·g~(-1)),表明以火山岩为填料的浸没式生物滤池反应器有利于ANAMMOX和AOB的协同生长,可快速实现SAND工艺的启动.     

进水浓度或HRT变化时微好氧处理微生态机制研究

考察改变进水COD浓度（11 000、 15 000、 30 000 mg/Ｌ）或水力停留时间（HRT为42 h、 25 h）对模拟高浓度有机废水微好氧连续小试处理效果的影响,并采用荧光原位杂交-流式细胞术（FISH-FCM）、聚合酶链式反应-变性梯度凝胶电泳(PCR-DGGE) 等分子生物学技术及Biolog　FF微孔板法分析了不同处理阶段稳定期曝气柱污泥的微生态变化,以探讨进水COD浓度或HRT改变时微好氧处理效果变化的微生态机制.结果表明,在全部4个处理阶段,曝气柱污泥中酵母含量均保持在＞99.9％的水平.随着进水COD浓度的上升,污泥浓度由2.0 g/Ｌ上升到7.3 g/Ｌ,COD比去除速度由2.3 kg/（kg·d）下降到1.7 kg/（kg·d）,曝气柱污泥真菌群落结构多样性指数由2.05上升至2.19,代谢多样性指数由4.42上升至4.45;而随着HRT下降,污泥浓度从7.3 g/Ｌ下降至6.0 g/Ｌ,COD比去除速度从1.7 kg/（kg·d）上升至2.8 kg/（kg·d）,真菌群落结构多样性指数和代谢多样性指数则分别从2.19和4.45降至0.79和4.36.作为提高进水有机负荷的主要措施,提高进水COD浓度和缩短HRT对于废水处理效果和曝气柱微生态存在截然相反的影响.     

Do land utilization patterns a ect methanotrophic communities in a Chinese upland red soil?

Soil samples were collected from three plots under di erent land utilization patterns including degradation, farming, and restoration. The abundances of methanotrophs were quantified using real-time polymerase chain reaction (PCR) based on the pmoA and 16S rRNA genes, and the community fingerprint was analyzed using denaturing gradient gel electrophoresis (DGGE) aiming at pmoA gene. Significantly lower 16S rRNA and pmoA genes copies were found in the degradation treatment than in farming and restoration. Higher abundances of Type I than those of Type II methanotrophs were detected in all treatments. The treatment of farming was clearly separated from degradation and restoration according to the DGGE profile by cluster analysis. The lowest diversity indices were observed in the F (farming plot), suggesting that the community structure was strongly a ected by farming activities. There were significantly positive correlations between the copy numbers of pmoA also Type II-related 16S rRNA genes and soil available K content. Strong negative and positive correlations were found between Type I and soil pH, and available P content, respectively. We concluded that the vegetation cover or not, soil characteristics including pH and nutrients of P and K as a result of anthropogenic disturbance may be key factors a ecting methanotrophic communities in upland soil.     

云南洱海沉积物中硫酸盐还原菌的时空分布特征

利用PCR扩增和荧光原位杂交方法分析了云南洱海沉积物中硫酸盐还原菌(Sulfate-reducing bacteria,SRB)类群和数量的时空分布特征。结果表明,秋季沉积物中检测出四个SRB类群(脱硫肠菌属、脱硫叶菌属、脱硫球菌属-脱硫线菌属-脱硫八叠菌属和脱硫弧菌属-脱硫微菌属),而春季沉积物中只检测出三个类群(脱硫肠菌属、脱硫叶菌属和脱硫球菌属-脱硫线菌属-脱硫八叠菌属)。相比春季,秋季沉积物检测出来的SRB类群具有更大的分布范围,同时,检测出的SRB类群主要分布在沉积物上部;从数量上来看,秋季沉积物SRB数量高于春季沉积物。上述结果指示秋季沉积物环境条件更适于SRB群落。此外,相比洱海秋季,洱海春季沉积环境溶解氧含量较高,且温度较低,这可能导致脱硫弧菌属-脱硫微菌属在洱海春季沉积物中处于不可育状态,由于其活性低而无法检测。     

绿色荧光蛋白标记在生物修复中的应用

通过对铜绿假单胞菌进行增强型绿色荧光蛋白(EGFP)标记,获得带有EGFP遗传标记的铜绿假单胞菌.该菌株绿色荧光标记性能稳定,通过转化子基因组DNAPCR和斑点杂交检测,证明外源EGFP基因存在于转化子染色体上.转化子30h内将溶液的表面张力由70mN/m降至35mN/m,产生的生物表面活性剂性能良好.