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Using pyrosequencing and quantitative PCR to analyze microbial communities

Husen ZHANG

Frontiers of Environmental Science & Engineering 2011, Volume 5, Issue 1,   Pages 21-27 doi: 10.1007/s11783-011-0303-9

Abstract: In parallel, quantitative real-time polymerase chain reaction (QPCR) allows quantitative monitoring of

Keywords： polymerase chain reaction (PCR)     microbial communities     pyrosequencing     gut     microbial fuel cell     sludge    

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Interaction and independence on methane oxidation of landfill cover soil among three impact factors: water, oxygen and ammonium

Pinjing HE, Na YANG, Wenjuan FANG, Fan Lü, Liming SHAO

Frontiers of Environmental Science & Engineering 2011, Volume 5, Issue 2,   Pages 175-185 doi: 10.1007/s11783-011-0320-8

Abstract: To understand the influence patterns and interactions of three important environmental factors, i.e. soil water content, oxygen concentration, and ammonium addition, on methane oxidation, the soils from landfill cover layers were incubated under full factorial parameter settings. In addition to the methane oxidation rate, the quantities and community structures of methanotrophs were analyzed to determine the methane oxidation capacity of the soils. Canonical correspondence analysis was utilized to distinguish the important impact factors. Water content was found to be the most important factor influencing the methane oxidation rate and Type II methanotrophs, and the optimum value was 15% (w/w), which induced methane oxidation rates 10- and 6- times greater than those observed at 5% (w/w) and 20% (w/w), respectively. Ambient oxygen conditions were more suitable for methane oxidation than 3% oxygen. The addition of of ammonium induced different effects on methane oxidation capacity when conducted at low or high water content. With regard to the methanotrophs, Type II was sensitive to the changes of water content, while Type I was influenced by oxygen content. Furthermore, the methanotrophic acidophile, , was detected in soils with a pH of 4.9, which extended their known living environments.

Keywords： quantitative polymerase chain reaction (PCR)     denaturing gradient gel electrophoresis (DGGE)     principal    

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Measurement and Control Technology for the Array of Low Cost PCR Microreactors

Li Xianming ,Zhang Yulin ,Li Jiantian

Strategic Study of CAE 2007, Volume 9, Issue 7,   Pages 76-81

Abstract:

In this paper a new style of polymerase chain reaction(PCR)equipmentIt is the concrete way to reduce the cost of PCR chips and improve the reliability of the chips.The measurement and control scheme for the low-cost PCR chips is designed.The uncertainty of indirect to the temperature of PCR liquid in low-cost PCR chips is also assessed.Its performance in temperature cycling meets the requirements of PCR.

Keywords： microreactors     measurement     control     polymerase chain reaction    

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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

Frontiers of Environmental Science & Engineering 2011, Volume 5, Issue 1,   Pages 28-39 doi: 10.1007/s11783-011-0302-x

Abstract: Real-time quantitative polymerase chain reaction (qPCR) has gained popularity as a technique to detect

Keywords： absolute quantification     design guideline     primer     probe     real-time quantitative polymerase chain reaction    

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Quantitative Analysis of the Effectiveness of Antigen- and Polymerase Chain Reaction-Based Combination Article

Qiangru Huang, Yanxia Sun, Mengmeng Jia, Ting Zhang, Fangyuan Chen, Mingyue Jiang, Qing Wang, Luzhao Feng, Weizhong Yang

Engineering 2023, Volume 28, Issue 9,   Pages 234-242 doi: 10.1016/j.eng.2023.01.004

Abstract: Antigen testing and its combination strategies were more efficient than polymerase chain reaction (PCRstrategies is the short turnaround time, which is also a critical factor to be optimized to improve PCR

Keywords： COVID-19     Antigen testing     PCR testing     Testing strategies    

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Seasonal microbial community shift in a saline sewage treatment plant

Qingmei YAN, Xuxiang ZHANG, Tong ZHANG, Herbert H P FANG

Frontiers of Environmental Science & Engineering 2011, Volume 5, Issue 1,   Pages 40-47 doi: 10.1007/s11783-011-0304-8

Abstract: community shift along with environmental variations using denaturing gradient gel electrophoresis of polymerasechain reaction amplified 16S rDNA fragments.

Keywords： sewage treatment plants     polymerase chain reaction (PCR)     denaturing gradient gel electrophoresis (DGGE    

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A pooling strategy of a PCR-based assay to detect Angiostrongylus cantonensis in snail intermediate host

Fu-Rong WEI MS, Shan LV PhD, He-Xiang LIU, Ling HU, Yi ZHANG MS,

Frontiers of Medicine 2010, Volume 4, Issue 2,   Pages 204-207 doi: 10.1007/s11684-010-0043-4

Abstract: number of assay and thus increase the efficiency in detecting and screening pathogen infections by polymerasechain reaction (PCR)-based assay.diagnosis of in Two settings of specimens were prepared, divided into portions and detected by multiplex PCR

Keywords： Angiostrongylus cantonensis     Pomacea canaliculata     multiplex polymerase chain reaction     diagnosis     pooling    

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Cultivation of aerobic granular sludge in a conventional, continuous flow, completely mixed activated sludge system

Xi CHEN,Linjiang YUAN,Wenjuan LU,Yuyou LI,Pei LIU,Kun NIE

Frontiers of Environmental Science & Engineering 2015, Volume 9, Issue 2,   Pages 324-333 doi: 10.1007/s11783-014-0627-3

Abstract: The microbial community structure of the granules was also analyzed by polymerase chain reaction-denaturinggradient gel electrophoresis (PCR-DGGE).

Keywords： sludge     completely mixed activated sludge system (CMAS)     continuous flow     shear force     filamentous bacteria     polymerasechain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)    

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A DNA Computing Model for the Graph Vertex Coloring Problem Based on a Probe Graph Article

Jin Xu, Xiaoli Qiang, Kai Zhang, Cheng Zhang, Jing Yang

Engineering 2018, Volume 4, Issue 1,   Pages 61-77 doi: 10.1016/j.eng.2018.02.011

Abstract: vertices in subgraphs; and②the bio-operation times are reduced considerably by a designed parallel polymerasechain reaction (PCR) technology that dramatically improves the processing speed.All these tiny strands are operated by DNA self-assembly and parallel PCR.After thousands of accurate PCR operations, the solutions were found by recognizing, splicing, and assembling

Keywords： DNA computing     Graph vertex coloring problem     Polymerase chain reaction    

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Erratum to: Using pyrosequencing and quantitative PCR to analyze microbial communities

Husen ZHANG

Frontiers of Environmental Science & Engineering 2011, Volume 5, Issue 3,   Pages 488-488 doi: 10.1007/s11783-011-0342-2

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involved in nitrogen cycling in wastewater treatment plants using DNA microarray and most probable number-PCR

Junqin PANG, Masami MATSUDA, Masashi KURODA, Daisuke INOUE, Kazunari SEI, Kei NISHIDA, Michihiko IKE

Frontiers of Environmental Science & Engineering 2016, Volume 10, Issue 4, doi: 10.1007/s11783-016-0846-x

Abstract: Numbers of , and genes were quantified by MPN-PCR.various processes of municipal WWTPs by employing two molecular-based methods:most probable number-polymerasechain reaction (MPN-PCR) and DNA microarray.MPN-PCR analysis revealed that gene quantities were not statistically different among processes, suggesting

Keywords： DNA microarray analysis     Nitrogen cycling functional genes     Most probable number-polymerase chain reaction(MPN-PCR)     Wastewater treatment plants (WWTPs)    

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An Evaluation Method of Human Gut Microbial Homeostasis by Testing Specific Fecal Microbiota Article

Zhongwen Wu, Xiaxia Pan, Yin Yuan, Pengcheng Lou, Lorina Gordejeva, Shuo Ni, Xiaofei Zhu, Bowen Liu, Lingyun Wu, Lanjuan Li, Bo Li

Engineering 2023, Volume 29, Issue 10,   Pages 110-119 doi: 10.1016/j.eng.2023.03.007

Abstract: characterized the whole microbiome in the human gut from a largesample Chinese cohort, constructed a real-time quantitativepolymerase chain reaction (qPCR) method and developed a set of analytical approaches to detect theseten groups of predominant gut bacterial species with great maneuverability, efficiency, and quantitative

Keywords： Gut microbiota     Machine learning     Microbial dysbiosis     Quantitative polymerase chain reaction     Chinese    

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Expression and clinical implication of PRL-1 and PRL-3 in transitional cell carcinoma of bladder

Bin HAO, Changwei LIU, Huixiang LI

Frontiers of Medicine 2009, Volume 3, Issue 2,   Pages 197-203 doi: 10.1007/s11684-009-0036-3

Abstract: The expression of PRL-1 and PRL-3 mRNA was detected by using reverse transcription polymerase chain reaction(RT-PCR) in 30 cases of BTCC and 10 cases of normal bladder, and the expression of PRL-1 and PRL-3 protein

Keywords： bladder     phosphatase of regenerating liver 1     phosphatase of regenerating liver 3     reverse transcription polymerasechain reaction     immunohistochemistry    

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A computational toolbox for molecular property prediction based on quantum mechanics and quantitative

Frontiers of Chemical Science and Engineering 2022, Volume 16, Issue 2,   Pages 152-167 doi: 10.1007/s11705-021-2060-z

Abstract: In this paper, a framework combining quantum mechanics and quantitative structure-property relationshippseudo experimental data), which are stored in a database and further provided for the developments of quantitativeTwo case studies highlighting different aspects of the toolbox involving the predictions of heats of reaction

Keywords： molecular property     quantum mechanics     quantitative structure-property relationship     heat of reaction    

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Continuous reaction performances of benzene alkylation with long chain olefins catalyzed by ionic liquid

QIAO Congzhen, LI Chengyue

Frontiers of Chemical Science and Engineering 2008, Volume 2, Issue 1,   Pages 69-73 doi: 10.1007/s11705-008-0014-3

Abstract: Based on a compulsive mixing-reacting-separating-recycling small experimental setup,the continuous reactionperformances of benzene alkylation with long chain olefins catalyzed by [BMIM]Cl-AlCl ionic liquid wereEven under the relatively hypecritical reaction conditions, the single pass conversion of pure 1-dodecene

Keywords： stability     different     hypecritical     compulsive mixing-reacting-separating-recycling     non-benzene    

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Title Author Date Type Operation

Using pyrosequencing and quantitative PCR to analyze microbial communities

Husen ZHANG

Journal Article

Interaction and independence on methane oxidation of landfill cover soil among three impact factors: water, oxygen and ammonium

Pinjing HE, Na YANG, Wenjuan FANG, Fan Lü, Liming SHAO

Journal Article

Measurement and Control Technology for the Array of Low Cost PCR Microreactors

Li Xianming ,Zhang Yulin ,Li Jiantian

Journal Article

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

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

Journal Article

Quantitative Analysis of the Effectiveness of Antigen- and Polymerase Chain Reaction-Based Combination

Qiangru Huang, Yanxia Sun, Mengmeng Jia, Ting Zhang, Fangyuan Chen, Mingyue Jiang, Qing Wang, Luzhao Feng, Weizhong Yang

Journal Article

Seasonal microbial community shift in a saline sewage treatment plant

Qingmei YAN, Xuxiang ZHANG, Tong ZHANG, Herbert H P FANG

Journal Article

A pooling strategy of a PCR-based assay to detect Angiostrongylus cantonensis in snail intermediate host

Fu-Rong WEI MS, Shan LV PhD, He-Xiang LIU, Ling HU, Yi ZHANG MS,

Journal Article

Cultivation of aerobic granular sludge in a conventional, continuous flow, completely mixed activated sludge system

Xi CHEN,Linjiang YUAN,Wenjuan LU,Yuyou LI,Pei LIU,Kun NIE

Journal Article

A DNA Computing Model for the Graph Vertex Coloring Problem Based on a Probe Graph

Jin Xu, Xiaoli Qiang, Kai Zhang, Cheng Zhang, Jing Yang

Journal Article

Erratum to: Using pyrosequencing and quantitative PCR to analyze microbial communities

Husen ZHANG

Journal Article

involved in nitrogen cycling in wastewater treatment plants using DNA microarray and most probable number-PCR

Junqin PANG, Masami MATSUDA, Masashi KURODA, Daisuke INOUE, Kazunari SEI, Kei NISHIDA, Michihiko IKE

Journal Article

An Evaluation Method of Human Gut Microbial Homeostasis by Testing Specific Fecal Microbiota

Zhongwen Wu, Xiaxia Pan, Yin Yuan, Pengcheng Lou, Lorina Gordejeva, Shuo Ni, Xiaofei Zhu, Bowen Liu, Lingyun Wu, Lanjuan Li, Bo Li

Journal Article

Expression and clinical implication of PRL-1 and PRL-3 in transitional cell carcinoma of bladder

Bin HAO, Changwei LIU, Huixiang LI

Journal Article

A computational toolbox for molecular property prediction based on quantum mechanics and quantitative

Journal Article

Continuous reaction performances of benzene alkylation with long chain olefins catalyzed by ionic liquid

QIAO Congzhen, LI Chengyue

Journal Article