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Soil Ecology Letters 2023年第1期5卷 142-150页

作者： Yixin Sun Xiaofang Du Yingbin Li Xu Han Shuai Fang Stefan Geisen Qi Li CAS Key Laboratory of Forest Ecology Management Institute of Applied EcologyChinese Academy of SciencesShenyang 110016China University of Chinese Academy of Sciences Beijing 100049China Laboratory of Nematology Wageningen UniversityWageningenThe Netherlands

High-throughput sequencing technology is increasingly used in the study of nematode biodiversity.However,the annotation difference of commonly used primers and reference databases on nematode community is still unclear.We compared two pairs of primers(3NDf/C_1132rmod,NF1F/18Sr2bR)and three databases(NT_V20200604,SILVA138/18s Eukaryota and PR2_v4.5 databases)on the determination of nematode community from four different vegetation types in Changbai Mountain,including mixed broadleaf-conifer forest,dark coniferous forest,betula ermanii Cham and alpine tundra.Our results showed that the selection of different primers and databases influenced the annotation of nematode taxa,but the diversity of nematode community showed consistent pattern among different vegetation types.Our findings emphasize that it is necessary to select appropriate primer and database according to the target taxonomic level.The difference in primers will affect the result of nematode taxa at different classification levels,so sequencing analysis cannot be used for comparison with studies using different primers.In terms of annotation effect in this study,3NDf/C_1132rmod primers with NT_v20200604 database could provide more information than other combinations at the genus or species levels.

关键词： Soil nematodes primer Database High-throughput sequencing Community composition

CRISPR primer Designer:Design primers for knockout and chromosome imaging CRISPR-Cas system

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Journal of Integrative Plant Biology 2015年第7期57卷 613-617页

作者： Meng Yan Shi-Rong Zhou Hong-Wei Xue National Key Laboratory of Plant Molecular Genetics Shanghai Institute of Plant Physiology and Ecologythe Chinese Academy of Sciences

The clustered regularly interspaced short palin- dromic repeats （CRiSPR）-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especially the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran locally and acquired a user- friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. We herein present researchers to design primers CRISPR primer Designer for for CRISPR applications. Theprogram has a user-frfendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR primer Designer runs locally and can be used to search spacer clusters, and exports primers for the CRiSPR-Cas system-based chromosome imaging system.

关键词： Chromosome imaging CRISPR knockout primer software

Effect of addition of chitosan to self-etching primer:antibacterial activity and push-out bond strength to radicular dentin

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The Journal of Biomedical Research 2012年第4期26卷 288-294页

作者： Shaymaa Elsaka Amr Elnaghy Department of Dental Biomaterials Faculty of DentistryMansoura University Department of Conservative Dentistry and Endodontics Faculty of DentistryMansoura University

The purpose of this study was to evaluate the antibacterial activity of a modified self-etching primer incorporating chitosan and whether this modification affected the bond strength to radicular dentin.A modified self-etching primer was prepared by adding chitosan solutions at 0.03%,0.06%,0.12% and 0.25%（W/W） to RealSeal selfetching primer.RealSeal primer without chitosan was used as the control.The antibacterial activity of the modified self-etching primer was evaluated using the direct contact test against Enterococcus faecalis.The bonding ability of the RealSeal system to radicular dentin was evaluated using the push-out bond strength test.The modes of failure were examined under a stereomicroscope.Data were analyzed using analysis of variance（ANOVA） and Tukey’s test,with a P-value 〈 0.05 indicating statistical significance.The results showed that the antibacterial properties of the freshly prepared and aged modified self-etching primer incorporating chitosan exhibited potent antibacterial effect against Enterococcus faecalis compared with the unmodified primer.The RealSeal system with the aged modified self-etching primer incorporating chitosan showed no significant differences in the bond strength as compared with the control（P = 0.99）.The findings suggest that modified self-etching primer incorporating chitosan is a promising antibacterial primer which does not adversely affect the bond strength of the RealSeal system to radicular dentin.

关键词： Enterococcus faecalis antibacterial activity chitosan push-out primer radicular dentin

多元统计软件primer在张网渔具种类选择性研究中的运用

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中国海洋大学学报（自然科学版） 2016年第8期46卷 37-46页

作者：李超张秀梅陈平李文涛中国海洋大学水产学院山东青岛266003

本文根据2014年秋季青岛斋堂岛海域双桩竖杆张网的网囊网目选择性试验数据,运用primer软件中的相似性分析、非参数多维标度分析和相似性百分比分析模块分析了张网渔具种类选择性。试验采用平行作业法,以传统网具(2a=16mm的菱形目网囊)... 详细信息

本文根据2014年秋季青岛斋堂岛海域双桩竖杆张网的网囊网目选择性试验数据,运用primer软件中的相似性分析、非参数多维标度分析和相似性百分比分析模块分析了张网渔具种类选择性。试验采用平行作业法,以传统网具(2a=16mm的菱形目网囊)作为对照网,设计了网目尺寸(2a)为30和35mm的菱形目网囊(以30D和35D表示)和网目尺寸(2a)为20、30和35mm的方形目网囊(以20S、30S和35S表示),进行选择性实验。研究显示:(1)35D、30S和35S渔获组成与对照网存在显著性差异,其余各网之间差异不显著。(2)改良后的试验网具能有效释放舒氏海龙;除20S组外,其余各试验网对方氏云鳚亦有较好的释放效果。(3)方形目网囊较相同尺寸的菱形目网囊具有更好的种类选择性;对相同网目形状的试验网囊进行比较,种类选择性随网目尺寸的增大而增大。(4)综合分析不同网具的渔获物组成和规格,在斋堂岛海域秋季小黄鱼、带鱼渔汛期,推荐使用30mm方形目网囊;方氏云鳚渔汛期,推荐使用20mm方形目网囊进行捕捞作业。研究结果表明,运用多元统计软件primer进行张网渔具种类选择性分析虽然存在待完善之处,但该方法为本领域研究提供了有益参考。

关键词： primer 多元统计分析张网菱形目网囊方形目网囊种类选择性

Development of Genomic Microsatellite Multiplex PCR Using Dye-Labeled Universal primer and Its Validation in Pedigree Analysis of Pacific Oyster(Crassostrea gigas)

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Journal of Ocean University of China 2017年第1期16卷 151-160页

作者： LIU Ting LI Qi SONG Junlin YU Hong Key Laboratory of Mariculture of Ministry of Education Ocean University of ChinaQingdao 266003P.R.China

There is an increasing requirement for traceability of aquaculture products, both for consumer protection and for food safety. There are high error rates in the conventional traceability systems depending on physical labels. Genetic traceability technique depending on DNA-based tracking system can overcome this problem. Genealogy information is essential for genetic traceability, and microsatellite DNA marker is a good choice for pedigree analysis. As increasing genotyping throughput of microsatellites, microsatellite multiplex PCR has become a fast and cost-effective technique. As a commercially important cultured aquatic species, Pacific oyster Crassostrea gigas has the highest global production. The objective of this study was to develop microsatellite multiplex PCR panels with dye-labeled universal primer for pedigree analysis in C. gigas, and these multiplex PCRs were validated using 12 full-sib families with known pedigrees. Here we developed six informative multiplex PCRs using 18 genomic microsatellites in C. gigas. Each multiplex panel contained a single universal primer M13(-21) used as a tail on each locus-specific forward primer and a single universal primer M13(-21) labeled with fluorophores. The polymorphisms of the markers were moderate, with an average of 10.3 alleles per locus and average polymorphic information content of 0.740. The observed heterozygosity per locus ranged from 0.492 to 0.822. Cervus simulations revealed that the six panels would still be of great value when massive families were analysed. Pedigree analysis of real offspring demonstrated that 100% of the offspring were unambiguously allocated to their parents when two multiplex PCRs were used. The six sets of multiplex PCRs can be an important tool for tracing cultured individuals, population genetic analysis, and selective breeding program in C. gigas.

关键词： Crassostrea gigas traceability microsatellites universal primer multiplex PCR pedigree analysis

禽流感病毒H5亚型及H7亚型基因的引物设计与多重RT-PCR扩增

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安徽农业科学 2008年第16期36卷 6689-6690页

作者：张文慧郭华王伟利刘明钱爱东吉林农业大学吉林长春130118 吉林出入境检验检疫局吉林长春130062 中国农业科学院哈尔滨兽医生物技术国家重点实验室黑龙江哈尔滨150001

[目的]设计能用于多重RT-PCR扩增禽流感病毒H5、H7亚型基因的引物。[方法]在GenBank中搜索H5、H7亚型禽流感病毒的基因序列,并利用DNAStar分析其同源性,采用primer Premier 5.0软件设计引物。[结果]多重RT-PCR扩增、琼脂糖凝胶电泳及测... 详细信息

[目的]设计能用于多重RT-PCR扩增禽流感病毒H5、H7亚型基因的引物。[方法]在GenBank中搜索H5、H7亚型禽流感病毒的基因序列,并利用DNAStar分析其同源性,采用primer Premier 5.0软件设计引物。[结果]多重RT-PCR扩增、琼脂糖凝胶电泳及测序结果显示引物设计成功。[结论]该方法用于禽流感病毒的快速诊断是可行的。

关键词：禽流感病毒 primer Premier 5.0 DNAStar 多重RT-PCR

Evolutionary pattern of 5'-UTR of enteroviruses and primer update for the detection of enteroviral RNA in environmental samples

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Asian Pacific Journal of Tropical Medicine 2012年第9期5卷 703-708页

作者： Nabil Ben Salem Abid Zyed Rouis Mahjoub Aouni Laboratoire des Maladies Transmissibles et Substances Biologiquement Actives LR99ES27 Faculte de Pharmacie de MonastirUniversite de MonastirAvenue Avicenne5000MonastirTunisie

Objective:To study the recombination events among enterovirus strains and the development of specific primers for the detection of enteroviruses in environmental samples.Methods: Nucleotide sequence analysis of enteroviruses deposited in the international database GenBank （www.***.nlm.***.gov/Genbank） was conducted to develop specific primers for the detection of these viruses.The specificity and sensitivity of the method were tested using coxackicvirus B3 strain Nancy,environmental isolate of human hepatitis A virus and human rotavirus strain WA.Seventy sewage samples were analyzed.Results:Enterovirus genome was detected in all positive samples.The genome of enterovirus was not detected in negative samples.The level of detection of these viruses was 102 TCID50mI..Conclusions:The development of new primers is an important issue for the detection of enteroviruses in the environment and the assessment of risk factors to human health.

关键词： Enterovirus RT-PCR Recombination primer update

SSR primer Screening for Marchantia convoluta by SAM Method

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Agricultural Biotechnology 2017年第5期6卷 1-5,10页

作者： Yuefeng WANG Fengfeng XIE Yuqing ZHOU Peilin DU Hua ZHU Jianbei TENG Chengdu University of Traditional Chinese Medicine Chengdu 610075China Guangxi University of Chinese Medicine Nanning 530200China First Affiliated Hospital of Guangxi University of Chinese Medicine Nanning 530023China

[Objectives] This study was conducted to study SSR primers in wild Marchantia convoluta by SAM method. [Methods] The M. convoluta genomic DNA was extracted by improved CTAB method,and the SSR primers for M. convoluta were selected through digestion,ligation,suppression PCR,pre-amplification,SAM method and PCR. [Results] The improved CTAB method extracted a high purity of DNA; the SAM PCR method gave clear bands; and 100 positive clones were sequenced,obtaining 86 sequences. [Conclusions] The SSR molecular markers could be used for analyzing the genetic diversity of M. convoluta.

关键词： Marchantia convoluta DNA extraction SAM method SSR primer screening

应用primer软件进行浮游植物群落结构的多元统计分析

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海洋与湖沼 2006年第4期37卷 316-321页

作者：吴荣军李瑞香朱明远郑家声郑有飞南京信息工程大学环境科学系南京210044 海洋生态环境科学与工程国家海洋局重点实验室青岛266061 中国海洋大学生命科学与技术学部青岛266003

根据青岛近海进行的一次添加营养盐的围隔实验数据,采用专业软件primer中的多元统计分析方法,进行了浮游植物群落结构的变化研究。结果表明,虽然由于本实验中浮游植物的生长受到Si的限制,硅藻类群不占明显的优势,使得优势种随时间的变... 详细信息

根据青岛近海进行的一次添加营养盐的围隔实验数据,采用专业软件primer中的多元统计分析方法,进行了浮游植物群落结构的变化研究。结果表明,虽然由于本实验中浮游植物的生长受到Si的限制,硅藻类群不占明显的优势,使得优势种随时间的变化不明显,没有出现明显的群落演替,但用primer软件的聚类分析(Clustering)和多维尺度转换排序(MDS)分析表明,添加营养盐后浮游植物群落结构有较明显的变化,同时,primer软件的相异系数(ANOSIM)分析也表明,在同时添加N、P的围隔内,浮游植物群落结构变化较只添加P的围隔中的变化显著。这显示了primer软件在分析浮游植物群落结构变化和评价水域富营养化中的应用前景。

关键词： primer 浮游植物群落结构多元统计

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ScYLV和SrMV的PCR引物优化设计

中国糖料 2012年第1期34卷 16-20,24页

作者：王洪星张雨良罗志文杨文君刘志昕中国热带农业科学院热带生物技术研究所/农业部热带作物生物技术重点开放实验室海口571101 海南大学环境与植物保护学院儋州571737

以甘蔗黄叶病毒(Sugarcane yellow leaf virus,,ScYLV)和高粱花叶病毒(Sorghum mosaic virus,,SrMV)为材料,运用DNAMAN、primer Premier 5.0和Oligo6.0等软件设计PCR引物,,进行普通PCR、多重PCR、实时定量PCR反应,检验所设计引物的PCR扩增效率、特异性和有效性。归纳总结多种PCR反应中引物设计的一般性思路,提出启发性的方法,并将以上经验付诸实践检验;最后将研究思路概括为:针对性、实用性和一般性。

关键词：甘蔗黄叶病毒高梁花叶病毒 PCR 引物设计 primer Premier 5.0 Oligo6.0 DNAMAN