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101.
[背景]嗜水气单胞菌(Aeromonas hydrophila)对水产动物、畜禽和人类均有致病性。基因表达的溶血素、气溶素和肠毒素是重要毒力因子,在致病性嗜水气单胞菌早期检测及防治中尤为重要。目前采用菌落直接提取DNA用于多重PCR研究的相关报道较少。[目的]基于菌落PCR方法建立针对嗜水气单胞菌溶血性基因、肠毒素基因和16S rRNA基因特异性片段(5个基因片段)的多重PCR快速检测方法。[方法]采用选择性RS (Rimler-Shotts)培养基对样品中嗜水气单胞菌有效富集分离和辨认,建立并优化嗜水气单胞菌16S rRNA、ast、alt、aerA、act这5个基因的多重PCR方法,比较菌落PCR中DNA模板不同提取方法对多重PCR扩增结果的影响,并检测该方法对维氏气单胞菌、温和气单胞菌、杀鲑气单胞菌的特异性。[结果]通过对RS培养基上单菌落的16S rRNA基因鉴定,初步判定嗜水气单胞菌和其他可培养菌的菌落形态,对其富集程度进行可视化辨别。多重PCR反应体系优化结果显示,引物浓度最优配比为16S rRNA:ast:alt:aerA:act=1:2:2:3:4。菌落PCR结果显示,... 相似文献
102.
【背景】生物受到温度胁迫时,热激蛋白被诱导并在短时间内大量产生,可以使受损的蛋白质恢复正常构象,增强生物对逆境胁迫的耐受性。【目的】初步探究草菇热激蛋白60(Vvhsp60)与低温耐受性的关系,为深入开展草菇不耐低温特性的遗传改良奠定理论基础。【方法】对Vvhsp60进行生物信息学分析,以低温敏感型草菇菌株V23及耐低温菌株VH3为实验材料,利用实时荧光定量PCR技术分析低温胁迫及热激诱导后在低温下草菇菌丝体中Vvhsp60基因的表达水平。【结果】草菇Vvhsp60编码蛋白不存在信号肽,不属于分泌蛋白,在线粒体和细胞质内发挥生物学作用,属于双向跨膜蛋白。低温处理显著提高了V23与VH3菌丝体中Vvhsp60基因的表达量,而且VH3中的表达量显著高于V23,推测Vvhsp60基因的表达量高可能有助于增强草菇对低温胁迫的耐受性。经热激处理后两菌株Vvhsp60基因的表达量显著高于各自未热激处理的对照组,表明热激处理可诱导Vvhsp60基因的表达。【结论】Vvhsp60与草菇低温耐受性相关,并且热激可以诱导Vvhsp60基因的表达。 相似文献
103.
【背景】猪链球菌(Streptococcus suis,SS)和猪多杀性巴氏杆菌(Pasteurella multocida,Pm)都是能引起宿主致病的人畜共患病原菌,常出现混合感染,临床诊断上易与猪瘟、猪丹毒等混淆。【目的】快速、有效鉴别猪链球菌病和猪多杀性巴氏杆菌病,建立一种能同时检测2种病原的多重实时荧光定量PCR检测方法。【方法】基于猪链球菌的gdh基因和猪多杀性巴氏杆菌的plpE基因,设计2对特异引物及TaqMan探针,以细菌16S rRNA基因设计通用引物及探针,通过对反应条件优化,建立了一种能同时检测猪链球菌和猪多杀性巴氏杆菌的多重实时荧光定量PCR检测方法。【结果】该方法能够特异性地检测猪链球菌和猪多杀性巴氏杆菌,与细菌分离后的测序结果验证完全一致。此方法对重组质粒标准品的最低检出浓度分别为4.53×102copies/μL和3.97×102copies/μL。重复性试验结果显示,该方法的组内和组间变异系数均小于3%。【结论】本实验所建立的方法准确、简便、可靠,能够用于2种病原菌的同时检测,为猪链球菌病和猪多杀性巴氏杆菌病的防治提供了有效的检测工具,具有重要的流行病学意义和临床应用价值。 相似文献
104.
Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in the last decade, almost solely relying on the 18S rRNA gene. As microbial eukaryotes are extremely diverse, many primers and primer pairs have been developed. To cover a relevant and representative fraction of the protist community in a given study system, an informed primer choice is necessary, as no primer pair can target all protists equally well. As such, a smart primer choice is very difficult even for experts and there are very few online resources available to list existing primers. We built a database listing 285 primers and 83 unique primer pairs that have been used for eukaryotic 18S rRNA gene metabarcoding. In silico performance of primer pairs was tested against two sequence databases: PR2 version 4.12.0 for eukaryotes and a subset of silva version 132 for bacteria and archaea. We developed an R -based web application enabling browsing of the database, visualization of the taxonomic distribution of the amplified sequences with the number of mismatches, and testing any user-defined primer or primer set ( https://app.pr2-primers.org ). Taxonomic specificity of primer pairs, amplicon size and location of mismatches can also be determined. We identified universal primer sets that matched the largest number of sequences and analysed the specificity of some primer sets designed to target certain groups. This tool enables guided primer choices that will help a wide range of researchers to include protists as part of their investigations. 相似文献
105.
Meng-Yao Li Bruno Ebel Fabrice Blanchard Cédric Paris Emmanuel Guedon Annie Marc 《Biotechnology and bioengineering》2019,116(5):985-993
The cell-specific growth rate (µ) is a critical process parameter for antibody production processes performed by animal cell cultures, as it describes the cell growth and reflects the cell physiological state. When there are changes in these parameters, which are indicated by variations of µ, the synthesis and the quality of antibodies are often affected. Therefore, it is essential to monitor and control the variations of µto assure the antibody production and achieve high product quality. In this study, a novel approach for on-line estimation of µ was developed based on the process analytical technology initiative by using an in situ dielectric spectroscopy. Critical moments, such as significant µ decreases, were successfully detected by this method, in association with changes in cell physiology as well as with an accumulation of nonglycosylated antibodies. Thus, this method was used to perform medium renewals at the appropriate time points, maintaining the values of µ close to its maximum. Using this method, we demonstrated that the physiological state of cells remained stable, the quantity and the glycosylation quality of antibodies were assured at the same time, leading to better process performances compared with the reference feed-harvest cell cultures carried out by using off-line nutrient measurements. 相似文献
106.
Identification of Campylobacter jejuni and determination of point mutations associated with macrolide resistance using a multiplex TaqMan MGB real‐time PCR 下载免费PDF全文
107.
A PCR assay for the quantification of growth of the oomycete pathogen Hyaloperonospora arabidopsidis in Arabidopsis thaliana 下载免费PDF全文
The accurate quantification of disease severity is important for the assessment of host–pathogen interactions in laboratory or field settings. The interaction between Arabidopsis thaliana and its naturally occurring downy mildew pathogen, Hyaloperonospora arabidopsidis (Hpa), is a widely used reference pathosystem for plant–oomycete interactions. Current methods for the assessment of disease severity in the Arabidopsis–Hpa interaction rely on measurements at the terminal stage of pathogen development; namely, visual counts of spore‐producing structures or the quantification of spore production with a haemocytometer. These assays are useful, but do not offer sensitivity for the robust quantification of small changes in virulence or the accurate quantification of pathogen growth prior to the reproductive stage. Here, we describe a quantitative real‐time polymerase chain reaction (qPCR) assay for the monitoring of Hpa growth in planta. The protocol is rapid, inexpensive and can robustly distinguish small changes in virulence. We used this assay to investigate the dynamics of early Hpa mycelial growth and to demonstrate the proof of concept that this assay could be used in screens for novel oomycete growth inhibitors. 相似文献
108.
André E. Minoche Juliane C. Dohm Jessica Schneider Daniela Holtgr?we Prisca Vieh?ver Magda Montfort Thomas Rosleff S?rensen Bernd Weisshaar Heinz Himmelbauer 《Genome biology》2015,16(1)
We develop a method to predict and validate gene models using PacBio single-molecule, real-time (SMRT) cDNA reads. Ninety-eight percent of full-insert SMRT reads span complete open reading frames. Gene model validation using SMRT reads is developed as automated process. Optimized training and prediction settings and mRNA-seq noise reduction of assisting Illumina reads results in increased gene prediction sensitivity and precision. Additionally, we present an improved gene set for sugar beet (Beta vulgaris) and the first genome-wide gene set for spinach (Spinacia oleracea). The workflow and guidelines are a valuable resource to obtain comprehensive gene sets for newly sequenced genomes of non-model eukaryotes.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-015-0729-7) contains supplementary material, which is available to authorized users. 相似文献109.
Konrad Zych Yang Li Joeri K van der Velde Ronny VL Joosen Wilco Ligterink Ritsert C Jansen Danny Arends 《BMC bioinformatics》2015,16(1)
Background
Genetic markers and maps are instrumental in quantitative trait locus (QTL) mapping in segregating populations. The resolution of QTL localization depends on the number of informative recombinations in the population and how well they are tagged by markers. Larger populations and denser marker maps are better for detecting and locating QTLs. Marker maps that are initially too sparse can be saturated or derived de novo from high-throughput omics data, (e.g. gene expression, protein or metabolite abundance). If these molecular phenotypes are affected by genetic variation due to a major QTL they will show a clear multimodal distribution. Using this information, phenotypes can be converted into genetic markers.Results
The Pheno2Geno tool uses mixture modeling to select phenotypes and transform them into genetic markers suitable for construction and/or saturation of a genetic map. Pheno2Geno excludes candidate genetic markers that show evidence for multiple possibly epistatically interacting QTL and/or interaction with the environment, in order to provide a set of robust markers for follow-up QTL mapping.We demonstrate the use of Pheno2Geno on gene expression data of 370,000 probes in 148 A. thaliana recombinant inbred lines. Pheno2Geno is able to saturate the existing genetic map, decreasing the average distance between markers from 7.1 cM to 0.89 cM, close to the theoretical limit of 0.68 cM (with 148 individuals we expect a recombination every 100/148=0.68 cM); this pinpointed almost all of the informative recombinations in the population.Conclusion
The Pheno2Geno package makes use of genome-wide molecular profiling and provides a tool for high-throughput de novo map construction and saturation of existing genetic maps. Processing of the showcase dataset takes less than 30 minutes on an average desktop PC. Pheno2Geno improves QTL mapping results at no additional laboratory cost and with minimum computational effort. Its results are formatted for direct use in R/qtl, the leading R package for QTL studies. Pheno2Geno is freely available on CRAN under “GNU GPL v3”. The Pheno2Geno package as well as the tutorial can also be found at: http://pheno2geno.nl.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-015-0475-6) contains supplementary material, which is available to authorized users. 相似文献110.
Jiaoping Zhang Qijian Song Perry B Cregan Randall L Nelson Xianzhi Wang Jixiang Wu Guo-Liang Jiang 《BMC genomics》2015,16(1)