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

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.     

Naphthalene emissions from moth repellents or toilet deodorant blocks determined using head-space and small-chamber tests

The present study investigated the emissions of naphthalene and other compounds from several different moth repellents(MRs) and one toilet deodorant block(TDB)currently sold in Korea,using a headspace analysis.The emission factors and emission rates of naphthalene were studied using a small-scale environmental chamber.Paper-type products emitted a higher concentration of the total volatile organic compounds(VOCs)(normalized to the weight of test piece)than ball-type products,which in turn emitted higher ...     

Deforestation and Avian Extinction on Tropical Landbridge Islands

Abstract: There are few empirical data, particularly collected simultaneously from multiple sites, on extinctions resulting from human‐driven land‐use change. Southeast Asia has the highest deforestation rate in the world, but the resulting losses of biological diversity remain poorly documented. Between November 2006 and March 2008, we conducted bird surveys on six landbridge islands in Malaysia and Indonesia. These islands were surveyed previously for birds in the early 1900s, when they were extensively forested. Our bird inventories of the islands were nearly complete, as indicated by sampling saturation curves and nonparametric true richness estimators. From zero (Pulau Malawali and Pulau Mantanani) to 15 (Pulau Bintan) diurnal resident landbird species were apparently extirpated since the early 1900s. Adding comparable but published extinction data from Singapore to our regression analyses, we found there were proportionally fewer forest bird extinctions in areas with greater remaining forest cover. Nevertheless, the statistical evidence to support this relationship was weak, owing to our unavoidably small sample size. Bird species that are restricted to the Indomalayan region, lay few eggs, are heavier, and occupy a narrower habitat breadth, were most vulnerable to extinction on Pulau Bintan. This was the only island where sufficient data existed to analyze the correlates of extinction. Forest preservation and restoration are needed on these islands to conserve the remaining forest avifauna. Our study of landbridge islands indicates that deforestation may increasingly threaten Southeast Asian biodiversity.     

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

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.     

考虑支座转角的地基不均匀沉降基础隔震结构地震响应分析∗

地基不均匀沉降可能会引起沉降范围内部分隔震支座发生转动,造成隔震层刚度发生变化,进而导致上部结构地震损伤和失效风险增大。针对地基不均匀沉降条件下基础隔震结构地震响应研究,现有成果大都通过施加平动位移进行模拟,并未考虑隔震支座转角的不利影响。为了研究地基不均匀沉降条件下基础隔震结构支座可能出现的转动及其对整体结构地震响应特征影响规律,首先以隔震支座为对象,研究了支座转动变形与叠层橡胶隔震支座水平刚度变化关系,建立了叠层橡胶隔震支座转角与水平刚度变化关系函数;在此基础上系统研究了地基不均匀沉降条件下整体基础隔震结构响应特征,以及基础结构的减震系数变化规律,以期揭示地基不均匀沉降对基础隔震结构地震响应影响机理。结果表明：隔震支座转角变形会引起隔震结构体系地震响应发生显著变化,随着隔震支座转角增大,隔震层水平刚度增大的同时隔震结构体系变形能力减弱,进而造成上部结构加速度响应增大,位移响应减小,导致基础隔震结构水平减震系数增大,减震效果低于预期;当转角接近π/2 时,隔震支座将丧失降低上部结构地震响应的作用,原隔震结构将退化为抗震结构;对于存在地基不均匀沉降的基础隔震结构,应及时采取必要措施控制地震响应,以防范上部结构发生倾覆。     

韩国绿色种养循环农业发展概况与经验启示

联合国将碳中和视为当今世界最为紧迫的任务，而农业是温室气体排放最多的产业之一，各国相继出台政策积极开展农业农村减排工作。韩国自2012年开始逐渐减少海洋粪污排泄量，并大力实行绿色种养循环农业，解决本国内畜禽粪污问题。韩国作为中国的重要海上邻国，不论是从研究借鉴角度抑或生态系统共享角度，了解其环境保护政策都是十分必要的。本文从韩国实施的主要政策、各地区农地养分收支现状、代表性运营模式案例、政策关注焦点等方面介绍韩国绿色种养循环农业的发展概况，结合中国绿色种养循环农业现状开展研究。提出三点政策建议：第一，进一步完善畜禽粪污资源化利用机具补贴辅助管理系统，提高系统在农户中的普及率；第二，提高全民环保意识的同时，政府的角色不应局限自上而下的引导型，应该积极促进种植户和养殖户间的自发组织，并大力提倡吸纳社会资本，集结社会各方力量；第三，促进绿色种养循环农业产品的商品化和品牌化，从而调动农户参与绿色种养循环农业的积极性。