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

Husen ZHANG

《环境科学与工程前沿（英文）》 2011年第5卷第3期页码 488-488 doi: 10.1007/s11783-011-0342-2

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Using pyrosequencing and quantitative PCR to analyze microbial communities

Husen ZHANG

《环境科学与工程前沿（英文）》 2011年第5卷第1期页码 21-27 doi: 10.1007/s11783-011-0303-9

摘要： New high-throughput technologies continue to emerge for studying complex microbial communities. In particular, massively parallel pyrosequencing enables very high numbers of sequences, providing a more complete view of community structures and a more accurate inference of the functions than has been possible just a few years ago. In parallel, quantitative real-time polymerase chain reaction (QPCR) allows quantitative monitoring of specific community members over time, space, or different environmental conditions. In this review, the principles of these two methods and their complementary applications in studying microbial ecology in bioenvironmental systems are discussed. The parallel sequencing of amplicon libraries and using barcodes to differentiate multiple samples in a pyrosequencing run are explained. The best procedures and chemistries for QPCR amplifications are also described and advantages of applying automation to increase accuracy are addressed. Three examples in which pyrosequencing and QPCR were used together to define and quantify members of microbial communities are provided: in the human large intestine, in a methanogenic digester whose sludge was made more bioavailable by a high-voltage pretreatment, and on the biofilm anode of a microbial electrolytic cell. The key findings in these systems and how both methods were used in concert to achieve those findings are highlighted.

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

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生物检测及分子诊断高端装备的研制及应用

彭年才,李磊,李政,苗保刚,李明,赵垚,蒋庄德

《中国工程科学》 2013年第15卷第1期页码 57-62

摘要：

以生物检测与分子诊断技术发展为背景，总结了团队在医学诊断、疾控、食品安全、检疫检验、生物学医学科学研究等领域的分子诊断高端装备的研制情况，重点介绍了实时荧光定量聚合酶链式反应（PCR）分子诊断仪关键技术的研发及仪器工程化技术

关键词：生物检测分子诊断实时荧光定量PCR ATP荧光检测

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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

《环境科学与工程前沿（英文）》 2011年第5卷第2期页码 175-185 doi: 10.1007/s11783-011-0320-8

摘要： 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.

关键词： quantitative polymerase chain reaction (PCR) denaturing gradient gel electrophoresis (DGGE) principal component analysis (PCA) canonical correspondence analysis (CCA)

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Assessment of antibiotic resistance genes in dialysis water treatment processes

Xuan Zhu, Chengsong Ye, Yuxin Wang, Lihua Chen, Lin Feng

《环境科学与工程前沿（英文）》 2019年第13卷第3期 doi: 10.1007/s11783-019-1136-1

摘要：

• Quantitative global ARGs profile in dialysis water was investigated.

• Totally 35 ARGs were found in the dialysis treatment train.

• 29 ARGs (highest) were found in carbon filtration effluent.

• erm and mtrD-02 occurred in the final effluent.

• The effluent was associated with health risks even after RO treatment.

关键词： Dialysis water Treatment process Antibiotic resistance gene High-throughput quantitative PCR Horizontal gene transfer

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Abundance and distribution of ammonia-oxidizing archaea in Tibetan and Yunnan plateau agricultural soils of China

Kun DING,Xianghua WEN,Liang CHEN,Daishi HUANG,Fan FEI,Yuyang LI

《环境科学与工程前沿（英文）》 2014年第8卷第5期页码 693-702 doi: 10.1007/s11783-014-0635-3

摘要： As low oxygen and high ultraviolet (UV) exposure might significantly affect the microbial existence in plateau, it could lead to a specialized microbial community. To determine the abundance and distribution of ammonia-oxidizing archaea (AOA) in agricultural soil of plateau, seven soil samples were collected respectively from farmlands in Tibet and Yunnan cultivating the wheat, highland-barley, and colza, which are located at altitudes of 3200–3800 m above sea level. Quantitative PCR (q-PCR) and clone library targeting on gene were used to quantify the abundances of AOA and ammonia-oxidizing bacteria (AOB), and characterize the community structures of AOA in the samples. The number of AOA cells (9.34 × 10 –2.32 × 10 g soil) was 3.86–21.84 times greater than that of AOB cells (6.91 × 10 –1.24 × 10 g soil) in most of the samples, except a soil sample cultivating highland-barley with an AOA/AOB ratio of 0.90. Based Kendall’s correlation coefficient, no remarkable correlation between AOA abundance and the environmental factor was observed. Additionally, the diversities of AOA community were affected by total nitrogen and organic matter concentration in soils, suggesting that AOA was probably sensitive to several environmental factors, and could adjust its community structure to adapt to the environmental variation while maintaining its abundance.

关键词： ammonia-oxidizing archaea ammonia-oxidizing bacteria quantitative PCR clone library plateau

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半滑舌鳎促黄体激素基因克隆和表达分析及其血清浓度测定

柳学周,史宝,王珊珊,徐永江,李晓晓

《中国工程科学》 2014年第16卷第9期页码 50-60

摘要：实时荧光定量组织表达分析表明，LH mRNA在脑、垂体、卵巢等组织中表达，垂体中表达量最丰富，其他组织尤以脑、性腺表达量较高，推测半滑舌鳎LH可能具有广泛的垂体外生理功能；实时荧光定量PCR方法对繁殖周期雌性半滑舌鳎

关键词：半滑舌鳎促黄体激素（LH） cDNA克隆实时荧光定量PCR 放射免疫测定

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基于抗原和聚合酶链式反应的组合策略对模拟社区内遏制COVID-19传播效果的定量分析 Article

黄蔷如, 孙艳侠, 贾萌萌, 张婷, 陈方圆, 姜明月, 王晴, 冯录召, 杨维中

《工程（英文）》 2023年第28卷第9期页码 234-242 doi: 10.1016/j.eng.2023.01.004

摘要：研究结果表明抗原检测及其组合策略比聚合酶链式反应（polymerase chain reaction, PCR）相关策略更高效，更有助于降低医院床位和重症监护病房床位需求。较短的结果返回时间是抗原检测策略的主要优势所在，也是优化PCR策略的关键因素。优化调整检测结果返回时间后，低频次的检测策略的效果可以媲美每日连续检测策略的效果。

关键词： COVID-19 抗原检测 PCR核酸检测检测策略

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低成本PCR微反应器阵列的温度测量与控制技术

李现明,张玉林,李建田

《中国工程科学》 2007年第9卷第7期页码 76-81

摘要：

设计了一种用于聚合酶链式反应的低成本微反应器，其内部无微加热器、微传感器。针对这种低成本的微反应器，提出了一种温度测量与控制方案，其特点是将各反应器温度的集中控制与分散控制有机结合，能够同时完成上百只微反应器快速、准确的温度循环。重点阐述了温度传感器负荷效应的提取与补偿、动态误差补偿、微反应器温度间接测量误差评定、微反应器温度串级控制策略。

关键词：微反应器测量控制聚合酶链式反应

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

《化学科学与工程前沿（英文）》 2022年第16卷第2期页码 152-167 doi: 10.1007/s11705-021-2060-z

摘要： Chemical industry is always seeking opportunities to efficiently and economically convert raw materials to commodity chemicals and higher value-added chemical-based products. The life cycles of chemical products involve the procedures of conceptual product designs, experimental investigations, sustainable manufactures through appropriate chemical processes and waste disposals. During these periods, one of the most important keys is the molecular property prediction models associating molecular structures with product properties. In this paper, a framework combining quantum mechanics and quantitative structure-property relationship is established for fast molecular property predictions, such as activity coefficient, and so forth. The workflow of framework consists of three steps. In the first step, a database is created for collections of basic molecular information; in the second step, quantum mechanics-based calculations are performed to predict quantum mechanics-based/derived molecular properties (pseudo experimental data), which are stored in a database and further provided for the developments of quantitative structure-property relationship methods for fast predictions of properties in the third step. The whole framework has been carried out within a molecular property prediction toolbox. Two case studies highlighting different aspects of the toolbox involving the predictions of heats of reaction and solid-liquid phase equilibriums are presented.

关键词： molecular property quantum mechanics quantitative structure-property relationship heat of reaction solid-liquid phase equilibrium

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Estimation of photolysis half-lives of dyes in a continuous-flow system with the aid of quantitative

Davoud BEIKNEJAD,Mohammad Javad CHAICHI

《环境科学与工程前沿（英文）》 2014年第8卷第5期页码 683-692 doi: 10.1007/s11783-014-0680-y

摘要： In this paper the photolysis half-lives of the model dyes in water solutions and under ultraviolet (UV) radiation were determined by using a continuous-flow spectrophotometric method. A quantitative structure-property relationship (QSPR) study was carried out using 21 descriptors based on different chemometric tools including stepwise multiple linear regression (MLR) and partial least squares (PLS) for the prediction of the photolysis half-life ( ) of dyes. For the selection of test set compounds, a K-means clustering technique was used to classify the entire data set, so that all clusters were properly represented in both training and test sets. The QSPR results obtained with these models show that in MLR-derived model, photolysis half-lives of dyes depended strongly on energy of the highest occupied molecular orbital ( ), largest electron density of an atom in the molecule ( ) and lipophilicity (log ). While in the model derived from PLS, besides aforementioned and descriptors, the molecular surface area ( ), molecular weight ( ), electronegativity ( ), energy of the second highest occupied molecular orbital ( ) and dipole moment ( ) had dominant effects on logt values of dyes. These were applicable for all classes of studied dyes (including monoazo, disazo, oxazine, sulfonephthaleins and derivatives of fluorescein). The results were also assessed for their consistency with findings from other similar studies.

关键词： dye photolysis half-life quantitative structure-property relationship continuous-flow stepwise multiple linear regression partial least squares

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Application of quantum chemical descriptors into quantitative structure-property relationship models

Yueping BAO, Qiuying HUANG, Wenlong WANG, Jiangjie XU, Fan JIANG, Chenghong FENG

《环境科学与工程前沿（英文）》 2011年第5卷第4期页码 505-511 doi: 10.1007/s11783-011-0318-2

摘要： Quantitative structure-property relationship (QSPR) models were developed for prediction of photolysis half-life ( ) of polychlorinated biphenyls (PCBs) in water under ultraviolet (UV) radiation. Quantum chemical descriptors computed by the PM3 Hamiltonian software were used as independent variables. The cross-validated value for the optimal QSPR model is 0.966, indicating good prediction capability for lg values of PCBs in water. The QSPR results show that the largest negative atomic charge on a carbon atom ( ) and the standard heat of formation (Δ ) have a dominant effect on values of PCBs. Higher values or lower Δ values of the PCBs leads to higher lg values. In addition, the lg values of PCBs increase with the increase in the energy of the highest occupied molecular orbital values. Increasing the largest positive atomic charge on a chlorine atom and the most positive net atomic charge on a hydrogen atom in PCBs leads to the decrease of lg values.

关键词： photolysis polychlorinated biphenyls (PCBs) quantitative structure-property relationships (QSPRs) quantum chemical descriptors

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Safety evaluation of microbial pesticide (HaNPV) based on PCR method

Miao Zhao, Shufei Li, Qinghong Zhou, Dianming Zhou, Ning He, Zhiyong Qian

《化学科学与工程前沿（英文）》 2019年第13卷第2期页码 377-384 doi: 10.1007/s11705-018-1777-9

摘要： Microbial pesticides can prevent and control diseases and pests of crops, and has become one of the important measures to ensure food and environmental safety. However, the potential harm of microbial pesticides to humans and animals is a serious concern at home and abroad. In this paper, we have investigated the infectivity and pathogenicity of a representative of viral microbial pesticides, helicoverpa armigera nuclear polyhedrosis virus (HaNPV), by specific and highly sensitive polymerase chain reaction technology. The results show that HaNPV can be gradually cleared in a short time after getting into blood of experimental rats, and does not infect other tissues or organs of animals; also indicate that the test subjects are not infectious to experimental rats after intravenous injection of HaNPV. Our method has good specificity and repeatability, and could provide an important reference for establishment of infectivity and pathogenicity detection methods for viral microbial pesticides in future.

关键词： microbial pesticides HaNPV acute intravenous injection infectivity pathogenicity

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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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Quantitative analysis of CO

Xianbing LIU, Can WANG

《环境科学与工程前沿（英文）》 2009年第3卷第1期页码 12-19 doi: 10.1007/s11783-009-0011-x

摘要： The increasing volume of CO embodiment in international trade adds a layer of complexity to environmental policies and has raised arguments on the traditional production based responsibility for CO emissions. In order to help understand the quantity of CO embodiment in trade and its policy implications, this paper gives observations to recently emerging literatures that quantitatively discuss CO embodiment in trade. The analytical approaches share the principle of using input and output modeling but vary dramatically in study boundary and estimation accuracy. The calculations can be roughly categorized into three types: direct quantification of CO embodiments in multiregional trade, direct quantification of CO embodiment in bilateral trade, and indirect analysis by comparing the scenarios with or without trade. The practical estimations strongly rely on trade partner selection and data availability. An obvious imbalance of net CO embodiment in the commodity trade between major developed countries and developing economies as a whole was confirmed by these literatures. Carbon taxes and other possible limitations on CO emissions have been addressed. The consistency across the calculations could be enhanced by systematic analyses in more detail to convince the international community to take binding commitments for the reduction of global CO emissions.

关键词： CO₂ embodiment international trade quantitative estimation analytical approach