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期刊论文 7

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2022 2

2020 2

2019 1

2016 1

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DNA组装 1

RT-qPCR 1

qPCR 1

二级结构 1

人源诺如病毒 1

优化设计 1

引物 1

探针 1

检测 1

组装效率 1

转化 1

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DNA组装效率的无偏差快速检验——基于qPCR而不依赖于转化的方法 Article

马晓焉, 梁昕鑫, 霍毅欣

《工程（英文）》 2019年 第5卷 第4期   页码 803-810 doi: 10.1016/j.eng.2019.06.002

摘要： 为快速、可靠地测定组装效率，本研究建立了一种基于qPCR的不依赖于转化的测定方法，用连接上的片段占初始加入片段的比例表征组装效率，3 h即可完成测定。这种基于qPCR的测定方法将促进DNA组装技术的发展，并有助于对组装效率影响因素的评估。

关键词： 组装效率     DNA组装     qPCR     二级结构     转化    

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检测GI和GII族人源诺如病毒双重RT-qPCR的优化设计 Article

刘丹蕾, 张子蕾, 吴清平, 田鹏, 耿浩然, 徐婷, 王大鹏

《工程（英文）》 2020年 第6卷 第4期   页码 442-448 doi: 10.1016/j.eng.2019.08.018

摘要： 为了提高HuNoV检出效率，本研究基于2010年后GenBank公布的病毒序列，分析设计了一套HuNoV检测引物和探针，并优化了一种新的双重RT-qPCR(new duplex RT-qPCR, ND-RT-qPCR以23份HuNoV临床样本为对象，评估了ND-RT-qPCR和常用RT-qPCR(Kageyama RT-qPCR)的检测性能。结果显示：ND-RT-qPCR检出所有GI族样本（5/5），而Kageyama RT-qPCR只检出两个样本（2/5）。ND-RT-qPCR检出18个GII族样本（18/18），而Kageyama RT-qPCR漏检1个样本。另外，ND-RTqPCR的灵敏度显著高于Kageyama RT-qPCR（前者Cq值低于后者Cq值）。因此，ND-RT-qPCR有助于提高HuNoV检出率，是目前该病毒检测良好的选择。

关键词： 人源诺如病毒     RT-qPCR     优化设计     引物     探针     检测    

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quantification of 3′-terminal 2′-O-methylated small RNAs by utilizing oxidative deep sequencing and stem-loop RT-qPCR

《医学前沿（英文）》 2022年 第16卷 第2期   页码 240-250 doi: 10.1007/s11684-021-0909-7

摘要： The continuing discoveries of novel classes of RNA modifications in various organisms have raised the need for improving sensitive, convenient, and reliable methods for quantifying RNA modifications. In particular, a subset of small RNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), are modified at their 3′-terminal nucleotides via 2′-O-methylation. However, quantifying the levels of these small RNAs is difficult because 2′-O-methylation at the RNA 3′-terminus inhibits the activity of polyadenylate polymerase and T4 RNA ligase. These two enzymes are indispensable for RNA labeling or ligation in conventional miRNA quantification assays. In this study, we profiled 3′-terminal 2′-O-methyl plant miRNAs in the livers of rice-fed mice by oxidative deep sequencing and detected increasing amounts of plant miRNAs with prolonged oxidation treatment. We further compared the efficiency of stem-loop and poly(A)-tailed RT-qPCR in quantifying plant miRNAs in animal tissues and identified stem-loop RT-qPCR as the only suitable approach. Likewise, stem-loop RT-qPCR was superior to poly(A)-tailed RT-qPCR in quantifying 3′-terminal 2′-O-methyl piRNAs in human seminal plasma. In summary, this study established a standard procedure for quantifying the levels of 3′-terminal 2′-O-methyl miRNAs in plants and piRNAs. Accurate measurement of the 3′-terminal 2′-O-methylation of small RNAs has profound implications for understanding their pathophysiologic roles in biological systems.

关键词： small RNAs     2′-O-methylation     sequencing     RT-qPCR    

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Bacterial inactivation, DNA damage, and faster ATP degradation induced by ultraviolet disinfection

Chao Yang, Wenjun Sun, Xiuwei Ao

《环境科学与工程前沿（英文）》 2020年 第14卷 第1期 doi: 10.1007/s11783-019-1192-6

摘要： • Long amplicon is more effective to test DNA damage induced by UV. • ATP in bacteria does not degrade instantly but does eventually after UV exposure. • After medium pressure UV exposure, ATP degraded faster. The efficacy of ultraviolet (UV) disinfection has been validated in numerous studies by using culture-based methods. However, the discovery of viable but non-culturable bacteria has necessitated the investigation of UV disinfection based on bacterial viability parameters. We used quantitative polymerase chain reaction (qPCR) to investigate DNA damage and evaluated adenosine triphosphate (ATP) to indicate bacterial viability. The results of qPCR effectively showed the DNA damage induced by UV when using longer gene amplicons, in that sufficiently long amplicons of both 16S and gadA indicated that the UV induced DNA damages. The copy concentrations of the long amplicons of 16S and gadA decreased by 2.38 log/mL and 1.88 log/mL, respectively, after exposure to 40 mJ/cm2 low-pressure UV. After UV exposure, the ATP level in the bacteria did not decrease instantly. Instead it decreased gradually at a rate that was positively related to the UV fluence. For low-pressure UV, this rate of decrease was slow, but for medium pressure UV, this rate of decrease was relatively high when the UV fluence reached 40 mJ/cm2. At the same UV fluence, the ATP level in the bacteria decreased at a faster rate after exposure to medium-pressure UV.

关键词： UV disinfection     DNA damage     qPCR     ATP    

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Effect of the ultraviolet/chlorine process on microbial community structure, typical pathogens, and antibiotic resistance genes in reclaimed water

《环境科学与工程前沿（英文）》 2022年 第16卷 第8期 doi: 10.1007/s11783-022-1521-z

摘要：

• UV/chlorine can effectively remove VBNC pathogens, ARGs and MGEs in reclaimed water.

关键词： UV/chlorine process     Pathogen     Antibiotic resistance genes     High-throughput qPCR     Reclaimed water    

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Design and use of group-specific primers and probes for real-time quantitative PCR

Juntaek LIM, Seung Gu SHIN, Seungyong LEE, Seokhwan HWANG

《环境科学与工程前沿（英文）》 2011年 第5卷 第1期   页码 28-39 doi: 10.1007/s11783-011-0302-x

摘要： Real-time quantitative polymerase chain reaction (qPCR) has gained popularity as a technique to detect and quantify a specific group of target microorganisms from various environmental samples including soil, water, sediments, and sludge. Although qPCR is a very useful technique for nucleic acid quantification, accurately quantifying the target microbial group strongly depends on the quality of the primer and probe used. Many aspects of conducting qPCR assays have become increasingly routine and automated; however, one of the most important aspects, designing and selecting primer and probe sets, is often a somewhat arcane process. In many cases, failed or non-specific amplification can be attributed to improperly designed primer-probe sets. This paper is intended to provide guidelines and general principles for designing group-specific primers and probes for qPCR assays. We demonstrate the effectiveness of these guidelines by reviewing the use of qPCR to study anaerobic processes and biologic nutrient removal processes. qPCR assays using group-specific primers and probes designed with this method, have been used to successfully quantify 16S ribosomal Ribonucleic Acid (16S rRNA) gene copy numbers from target methanogenic and ammonia- oxidizing bacteria in various laboratory- and full-scale biologic processes. Researchers with a good command of primer and probe design can use qPCR as a valuable tool to study biodiversity and to develop more efficient control strategies for biologic processes.

关键词： absolute quantification     design guideline     primer     probe     real-time quantitative polymerase chain reaction (qPCR)    

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Analysis of differential expression of genes induced by ethephon in elongating internodes of maize plants

Xiaoyi WEI,Weiqiang ZHANG,Qian ZHANG,Pei SUN,Zhaohu LI,Mingcai ZHANG,Jianmin LI,Liusheng DUAN

《农业科学与工程前沿（英文）》 2016年 第3卷 第3期   页码 263-282 doi: 10.15302/J-FASE-2016103

摘要： Plant growth regulators (PGRs) are commonly used in cereal cropping systems to restrict plant height and control lodging. Ethephon has been reported to shorten internodes and increase grain yield of maize. To analyze the transcriptomic profiles of maize internode elongation following ethephon treatment, differentially expressed genes were compared between the treatment and control samples of inbred line Zong 31 using the Affymetrix Maize Genome Array. According to the microarray data, 326 probe sets showed significant change in expression. Further research revealed that the most remarkable effects of ethephon on maize internodes elongation occurred during a 48 h period, when 89 differentially expressed genes were detected. There were dramatic change in transcript levels at 24 h and six Auxin transport genes and four gibberellin biosynthesis pathway genes were differentially expressed in Zong 31 in response to ethephon treatment. In summary, we showed that gaseous ethylene release is involved in internode meristem cell elongation through the regulation of plant hormone signaling in maize. This work provides a platform for studies in which candidate genes will be functionally tested for involvement in internode elongation.

关键词： maize     ethephon     internode elongation     microarray     qPCR    

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标题 作者 时间 类型 操作

DNA组装效率的无偏差快速检验——基于qPCR而不依赖于转化的方法

马晓焉, 梁昕鑫, 霍毅欣

期刊论文

检测GI和GII族人源诺如病毒双重RT-qPCR的优化设计

刘丹蕾, 张子蕾, 吴清平, 田鹏, 耿浩然, 徐婷, 王大鹏

期刊论文

quantification of 3′-terminal 2′-O-methylated small RNAs by utilizing oxidative deep sequencing and stem-loop RT-qPCR

期刊论文

Bacterial inactivation, DNA damage, and faster ATP degradation induced by ultraviolet disinfection

Chao Yang, Wenjun Sun, Xiuwei Ao

期刊论文

Effect of the ultraviolet/chlorine process on microbial community structure, typical pathogens, and antibiotic resistance genes in reclaimed water

期刊论文

Design and use of group-specific primers and probes for real-time quantitative PCR

Juntaek LIM, Seung Gu SHIN, Seungyong LEE, Seokhwan HWANG

期刊论文

Analysis of differential expression of genes induced by ethephon in elongating internodes of maize plants

Xiaoyi WEI,Weiqiang ZHANG,Qian ZHANG,Pei SUN,Zhaohu LI,Mingcai ZHANG,Jianmin LI,Liusheng DUAN

期刊论文