Applicability of PCR-DGGE and 16S rDNA Sequencing for Microbiological Analysis of Otitis Media with Effusion

Background: The aim of the study was to analyze the performance of PCR-DGGE based assay and its applicability as a tool for the identification of bacteria in the middle ear of children with otitis media with effusion (OME). Methods: The middle ear effusions from 20 children with OME were analyzed both by bacterial culture and by 16S rDNA-gene-targeted PCR assay, DGGE fingerprinting and sequencing analysis. Results: In bacterial culture assay, only three middle ear effusions (15%) showed bacterial growth. None of the samples were positive for anaerobic culture. The PCR assay with 16S rDNA-gene-targeted universal primers was positive in 10 (50%) cases. The subsequent DGGE fingerprinting and 16S rDNA sequencing analysis revealed that the most commonly encountered bacteria in the middle ear effusions of children with OME are Haemophilus influenzae, Alloiococcus otitidis and Bacteroides spp. Conclusions: The present study demonstrated the applicability of PCR-DGGE based assay and 16S rDNA sequencing for analyzing of bacterial diversity in the middle ear effusion of children OME. The results of our study may contribute to a better understanding of the etiology of OME.

东方拟无枝酸菌中vcm14基因的敲除对万古霉素合成的影响

PCR-targeting是一种用于敲除或阻断放线菌染色体上某一基因的快速高效的方法。本研究利用该方法在大肠埃希菌中构建破坏粘粒cLYLH17(Δvcm14::apr),通过结合转移首次敲除东方拟无枝酸菌HCCB10007中万古霉素生物合成基因簇中推测的haloperoxidase基因——vcm14,得到一株双交换阻断突变株A.orientalis dvcm14(Δvcm14::apr)。该菌不产生万古霉素及其类似物,证实vcm14基因的编码蛋白不是haloperoxidase,且该蛋白不参与万古霉素的卤化反应,可能是万古霉素生物合成途径中的一个关键酶。本研究为阐明万古霉素生物合成途径中的卤化过程提供了有益线索。

Evaluation of pharmaceutical activities of G-protein coupled receptor targeted pharmaceuticals in Chinese wastewater effluent

The occurre nce of biologically active pharmaceuticals in aquatic enviro nments raised the potential risks to aquatic species.Among these marketed biological active pharmaceuticals,it has been estimated that40%of them target G-protein-coupled receptors(GPCRs).We have illustrated pharmaceutical activities of GPCR targeted pharmaceuticals in English and Japanese wastewater by the in vitro transforming growth factor-α(TGFα)shedding assay.However,as the most important producer and consumer of pharmaceuticals,the occurrence of GPCR targeted pharmaceuticals in China had remained unclear.In this study,we investigated the pharmaceutical activities of GPCR targeted pharmaceuticals in secondary effluents of Chinese wastewater treatment plants.We discovered antagonistic activities against angiotensin(AT1)receptor at up to 7.2×102 ng-valsartan-equivalent quantity/L in Chinese wastewater for the first time as well as agonistic activities against dopamine(D2)receptor.Furthermore,in parallel with the assay,we determined concentrations of GPCR targeted pharmaceuticals in target wastewater by liquid chromatography coupled with tandem mass spectrometry(LC-MS/MS).Through the comparison of predicted antagonistic activities calculated by concentrations and potency values from the assay,we found that the measured antagonistic activities against AT1 receptor from the assay were higher than the predicted AT1 activities from valsartan,irbesartan,and losartan,indicating the potential existence of other unknown AT1 antagonists in wastewater.

一个硫链丝菌素抗性基因标记、用于DNA导入链霉菌的pSET152衍生载体(英文)

【目的】在链霉菌PCR-targeting系统中,安普霉素是使用最普遍的选择标记。然而在基因敲除阶段利用安普霉素选择标记后,在遗传补偿时就不能使用相同选择标记的许多重要载体,如pSET152。这常给研究带来不便,特别是当研究对象基因如一些调控基因,其生理功能对剂量敏感时更是如此。基于此,拟以pSET152为基础构建一个不以安普霉素为抗性标记的通用整合型载体。【方法】利用融合PCR和λRed重组等方法构建载体。【结果】来自pHZ1358上的硫链丝菌素抗性基因tsr和来自pCR2.1的氨苄抗性基因bla以"tsr在前bla在后"的次序融合。融合后的抗性片段替换pSET152上的安普霉素抗性基因aac(3)-IV,从而获得新载体pGIM6626。利用该载体将删除的榴菌素最小聚酮合酶基因重新导入到Streptomyces vietnamensis突变株中,该突变株恢复了产榴菌素的能力,证实了该载体的有效性。【结论】构建了一个新的pSET152衍生载体pGIM6626。该载体包含氨苄和硫链丝菌素抗性基因,分别在大肠杆菌和链霉菌中作为选择标记。pGIM6626与pSET152用途相似,但前者由于与PCR-targeting系统不存在选择标记的冲突而与该系统更兼容。

东方拟无枝酸菌HCCB10007中vcm8基因的敲除及无氯万古霉素产生菌的构建

目的:利用基因敲除的方法构建无氯万古霉素产生菌。方法:利用PCR-Targeting的方法获得破坏粘粒cLYLH15(Δvcm8::apr),通过接合转移敲除东方拟无枝酸菌HCCB10007中万古霉素生物合成基因簇中的卤化酶基因vcm8。结果:筛选得到1株突变子A.orientalisdvcm8(Δvcm8::apr)。结论:该菌不再代谢产生万古霉素,转而合成无氯万古霉素。经传代试验证明该菌株遗传稳定,可作为无氯万古霉素产生菌。

Reconstruction of a hybrid nucleoside antibiotic gene cluster based on scarless modification of large DNA fragments

Genetic modification of large DNA fragments(gene clusters) is of great importance in synthetic biology and combinatorial biosynthesis as it facilitates rational design and modification of natural products to increase their value and productivity.In this study,we developed a method for scarless and precise modification of large gene clusters by using RecET/RED-mediated polymerase chain reaction(PCR) targeting combined with Gibson assembly.In this strategy,the biosynthetic genes for peptidyl moieties(HPHT) in the nikkomycin biosynthetic gene cluster were replaced with those for carbamoylpolyoxamic acid(CPOAA)from the polyoxin biosynthetic gene cluster to generate a^40 kb hybrid gene cluster in Escherichia coli with a reusable targeting cassette.The reconstructed cluster was introduced into Streptomyces lividans TK23 for heterologous expression and the expected hybrid antibiotic,polynik A,was obtained and verified.This study provides an efficient strategy for gene cluster reconstruction and modification that could be applied in synthetic biology and combinatory biosynthesis to synthesize novel bioactive metabolites or to improve antibiotic production.