Journal of biomolecular techniques : JBT最新文献_第5页

Article Watch: December 2018. 文章观察:2018年12月。

Journal of biomolecular techniques : JBT Pub Date : 2018-12-01 DOI: 10.7171/jbt.18-2904-001

C. Slaughter

引用次数: 0

Article Watch: September 2018. 文章观察:2018年9月。

Journal of biomolecular techniques : JBT Pub Date : 2018-09-01 DOI: 10.7171/jbt.18-2903-004

C. Slaughter

引用次数: 0

Article Watch: July 2018. 文章观察:2018年7月。

Journal of biomolecular techniques : JBT Pub Date : 2018-07-01 DOI: 10.7171/jbt.18-2902-004

C. Slaughter

引用次数: 0

Article Watch: April 2018. 文章观察:2018年4月。

Journal of biomolecular techniques : JBT Pub Date : 2018-04-01 DOI: 10.7171/jbt.18-2901-004

C. Slaughter

引用次数: 0

CTLS-2016 and the Formation of a Pan-European Professional Society through the Lens of an ABRF Founding Member. CTLS-2016和泛欧洲专业协会的形成，通过一个ABRF创始成员的镜头。

Journal of biomolecular techniques : JBT Pub Date : 2017-01-05 DOI: 10.7171/jbt.17-2801-002

R. Niece

引用次数: 0

Core Technologies in Life Sciences (CTLS) 2016 Conference Summary. 生命科学核心技术(CTLS) 2016年会总结。

Journal of biomolecular techniques : JBT Pub Date : 2016-12-01 DOI: 10.7171/JBT.16-2704-003

J. Rappoport

引用次数: 1

Article Watch: December 2016. 文章观察:2016年12月。

Journal of biomolecular techniques : JBT Pub Date : 2016-12-01 DOI: 10.7171/JBT.16-2704-004

C. Slaughter

引用次数: 0

Automated Sanger Analysis Pipeline (ASAP): A Tool for Rapidly Analyzing Sanger Sequencing Data with Minimum User Interference. 自动化桑格分析管道(ASAP):一种以最小用户干扰快速分析桑格测序数据的工具。

Journal of biomolecular techniques : JBT Pub Date : 2016-10-17 DOI: 10.7171/JBT.16-2704-005

Aditya Singh, P. Bhatia

{"title":"Automated Sanger Analysis Pipeline (ASAP): A Tool for Rapidly Analyzing Sanger Sequencing Data with Minimum User Interference.","authors":"Aditya Singh, P. Bhatia","doi":"10.7171/JBT.16-2704-005","DOIUrl":"https://doi.org/10.7171/JBT.16-2704-005","url":null,"abstract":"Sanger sequencing platforms, such as applied biosystems instruments, generate chromatogram files. Generally, for 1 region of a sequence, we use both forward and reverse primers to sequence that area, in that way, we have 2 sequences that need to be aligned and a consensus generated before mutation detection studies. This work is cumbersome and takes time, especially if the gene is large with many exons. Hence, we devised a rapid automated command system to filter, build, and align consensus sequences and also optionally extract exonic regions, translate them in all frames, and perform an amino acid alignment starting from raw sequence data within a very short time. In full capabilities of Automated Mutation Analysis Pipeline (ASAP), it is able to read \"*.ab1\" chromatogram files through command line interface, convert it to the FASTQ format, trim the low-quality regions, reverse-complement the reverse sequence, create a consensus sequence, extract the exonic regions using a reference exonic sequence, translate the sequence in all frames, and align the nucleic acid and amino acid sequences to reference nucleic acid and amino acid sequences, respectively. All files are created and can be used for further analysis. ASAP is available as Python 3.x executable at https://github.com/aditya-88/ASAP. The version described in this paper is 0.28.","PeriodicalId":94326,"journal":{"name":"Journal of biomolecular techniques : JBT","volume":"1 1","pages":"129-131"},"PeriodicalIF":0.0,"publicationDate":"2016-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82933766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

Establishment of a Simple and Quick Method for Detecting Extended-Spectrum β-Lactamase (ESBL) Genes in Bacteria. 细菌β-内酰胺酶(ESBL)扩谱基因快速检测方法的建立

Journal of biomolecular techniques : JBT Pub Date : 2016-09-16 DOI: 10.7171/JBT.16-2704-001

Song-Tao Han, Y. Fei, Jin-You Huang, Mei Xu, Li-Chan Chen, D. Liao, Yujie Tan

{"title":"Establishment of a Simple and Quick Method for Detecting Extended-Spectrum β-Lactamase (ESBL) Genes in Bacteria.","authors":"Song-Tao Han, Y. Fei, Jin-You Huang, Mei Xu, Li-Chan Chen, D. Liao, Yujie Tan","doi":"10.7171/JBT.16-2704-001","DOIUrl":"https://doi.org/10.7171/JBT.16-2704-001","url":null,"abstract":"Extended-spectrum β-lactamase (ESBL) genes that render bacteria resistant to antibiotics are commonly detected using phenotype testing, which is time consuming and not sufficiently accurate. To establish a better method, we used phenotype testing to identify ESBL-positive bacterial strains and conducted PCR to screen for TEM (named after the patient Temoneira who provided the first sample), sulfhydryl reagent variable (SHV), cefotaxime (CTX)-M-1, and CTX-M-9, the 4 most common ESBL types and subtypes. We then performed multiplex PCR with 1 primer containing a biotin and hybridized the PCR products with gene-specific probes that were coupled with microbeads and coated with a specific fluorescence. The hybrids were linked to streptavidin-R-phycoerythrins (SA-PEs) and run through a flow cytometer, which sorted the fluorescently dyed microbeads and quantified the PEs. The results from single PCR, multiplex PCR, and cytometry were consistent with each other. We used this method to test 169 clinical specimens that had been determined for phenotypes and found 154 positive for genotypes, including 30 of the 45 samples that were negative for phenotypes. The CTX-M genotype tests alone, counting both positive and negative cases, showed 99.41% (168/169) consistency with the ESBL phenotype test. Thus, we have established a multiplex-PCR system as a simple and quick method that is high throughput and accurate for detecting 4 common ESBL types and subtypes.","PeriodicalId":94326,"journal":{"name":"Journal of biomolecular techniques : JBT","volume":"1 1","pages":"132-137"},"PeriodicalIF":0.0,"publicationDate":"2016-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83229584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Monitoring Error Rates In Illumina Sequencing. Illumina测序中的错误率监测。

Journal of biomolecular techniques : JBT Pub Date : 2016-09-16 DOI: 10.7171/JBT.16-2704-002

Leigh J. Manley, Duanduan Ma, S. Levine

{"title":"Monitoring Error Rates In Illumina Sequencing.","authors":"Leigh J. Manley, Duanduan Ma, S. Levine","doi":"10.7171/JBT.16-2704-002","DOIUrl":"https://doi.org/10.7171/JBT.16-2704-002","url":null,"abstract":"Guaranteeing high-quality next-generation sequencing data in a rapidly changing environment is an ongoing challenge. The introduction of the Illumina NextSeq 500 and the depreciation of specific metrics from Illumina's Sequencing Analysis Viewer (SAV; Illumina, San Diego, CA, USA) have made it more difficult to determine directly the baseline error rate of sequencing runs. To improve our ability to measure base quality, we have created an open-source tool to construct the Percent Perfect Reads (PPR) plot, previously provided by the Illumina sequencers. The PPR program is compatible with HiSeq 2000/2500, MiSeq, and NextSeq 500 instruments and provides an alternative to Illumina's quality value (Q) scores for determining run quality. Whereas Q scores are representative of run quality, they are often overestimated and are sourced from different look-up tables for each platform. The PPR's unique capabilities as a cross-instrument comparison device, as a troubleshooting tool, and as a tool for monitoring instrument performance can provide an increase in clarity over SAV metrics that is often crucial for maintaining instrument health. These capabilities are highlighted.","PeriodicalId":94326,"journal":{"name":"Journal of biomolecular techniques : JBT","volume":"19 1","pages":"125-128"},"PeriodicalIF":0.0,"publicationDate":"2016-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89702730","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 61