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UK Biobank: what can it do, how you can use it and how is it being used?
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2025-01-23 DOI: 10.1080/07366205.2024.2441639
Tristan Free
{"title":"UK Biobank: what can it do, how you can use it and how is it being used?","authors":"Tristan Free","doi":"10.1080/07366205.2024.2441639","DOIUrl":"https://doi.org/10.1080/07366205.2024.2441639","url":null,"abstract":"","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"1-5"},"PeriodicalIF":2.2,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Analytical validation of the IBD segment-based tool KinSNP® for human identification applications. 基于IBD片段的工具KinSNP®用于人类鉴定应用的分析验证。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2025-01-18 DOI: 10.1080/07366205.2025.2454770
Bruce Budowle, Jianye Ge, Lee Baker, Kristen Mittelman, David Mittelman
{"title":"Analytical validation of the IBD segment-based tool KinSNP<sup>®</sup> for human identification applications.","authors":"Bruce Budowle, Jianye Ge, Lee Baker, Kristen Mittelman, David Mittelman","doi":"10.1080/07366205.2025.2454770","DOIUrl":"https://doi.org/10.1080/07366205.2025.2454770","url":null,"abstract":"<p><p>KinSNP<sup>®</sup> v1.0, a software tool for human identification, has been widely used to measure IBD segment sharing between individuals using dense SNP data. Herein, the tool was validated using simulated pedigree data (up to 9<sup>th</sup> degree relationships) from five diverse populations from the 1000 Genomes Project. Performance was further tested under conditions of simulated genotyping errors and allele or locus dropout. KinSNP data were benchmarked with IBIS, Ped-sim, and known ranges of centimorgan sharing. The calculated values from KinSNP aligned closely with IBIS and Ped-sim benchmarks, and accuracy was maintained with up to 75% simulated missing data. However, even slight increases in simulated sequence error rates negatively impacted performance. This study supports that KinSNP is a reliable solution for IBD-based analyses in forensic contexts.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"1-14"},"PeriodicalIF":2.2,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142999164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Correction. 修正。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2025-01-16 DOI: 10.1080/07366205.2025.2450187
{"title":"Correction.","authors":"","doi":"10.1080/07366205.2025.2450187","DOIUrl":"https://doi.org/10.1080/07366205.2025.2450187","url":null,"abstract":"","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"1-2"},"PeriodicalIF":2.2,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142999302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Enhanced Blastocystis subtyping from stool samples using semi-nested barcode PCR: validation with an NGS-based approach. 利用半嵌套条形码PCR从粪便样本中增强囊虫亚型：基于ngs方法的验证。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-12-27 DOI: 10.1080/07366205.2024.2442835
Carlos Nieto-Clavijo, Liliana Morales, Andrés Delgado-Aldana, Paula C Hernández, Isabel Torres-Molina, Amanda Gonzalez-Cuiza, Fabián Cortés-Muñoz, Jacqueline Chaparro-Olaya
{"title":"Enhanced <i>Blastocystis</i> subtyping from stool samples using semi-nested barcode PCR: validation with an NGS-based approach.","authors":"Carlos Nieto-Clavijo, Liliana Morales, Andrés Delgado-Aldana, Paula C Hernández, Isabel Torres-Molina, Amanda Gonzalez-Cuiza, Fabián Cortés-Muñoz, Jacqueline Chaparro-Olaya","doi":"10.1080/07366205.2024.2442835","DOIUrl":"https://doi.org/10.1080/07366205.2024.2442835","url":null,"abstract":"<p><p>In 2006, a PCR method was introduced to subtype <i>Blastocystis</i> by Sanger sequencing of an ≈610 bp amplicon of the 18S rRNA gene. This method, known as barcoding-PCR, has become widespread, although the primer pair used can amplify non-<i>Blastocystis</i> sequences, which can result in false positives. Barcoding-PCR is most effective with DNA extracted from <i>Blastocystis</i> cultures, limiting its sensitivity when used directly with stool samples. As a result, barcoding-PCR can sometimes yield negative results for stool samples confirmed as <i>Blastocystis</i>-positive by microscopy. To improve subtyping from stool-derived DNA, we developed a Semi-Nested barcode PCR that amplifies the barcoding region in a second reaction. Our study shows that this Semi-Nested approach outperforms classical barcoding-PCR, detecting <i>Blastocystis</i> more reliably from stool samples with stronger gel signals and no false positives. This was confirmed by near-complete concordance (68/70 samples) with the Santin-PCR coupled to Next-Generation Sequencing (NGS) as reference standard for <i>Blastocystis</i> subtyping. Of particular interest, one amplicon matched the only previous report of ST35, marking this as the second global detection of ST35 and the first in Colombia. Overall, Semi-Nested barcoded PCR offers a more robust and sensitive alternative compared to classical barcoding-PCR for subtyping <i>Blastocystis</i> directly from stool samples.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"1-11"},"PeriodicalIF":2.2,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142891815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
qDATA - an R application implementing a practical framework for analyzing quantitative real-time PCR data. qDATA -一个R应用程序，实现了分析实时定量PCR数据的实用框架。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-12-24 DOI: 10.1080/07366205.2024.2442217
Adrian Ionascu, Alexandru Al Ecovoiu, Mariana Carmen Chifiriuc, Attila Cristian Ratiu
{"title":"qDATA - an R application implementing a practical framework for analyzing quantitative real-time PCR data.","authors":"Adrian Ionascu, Alexandru Al Ecovoiu, Mariana Carmen Chifiriuc, Attila Cristian Ratiu","doi":"10.1080/07366205.2024.2442217","DOIUrl":"https://doi.org/10.1080/07366205.2024.2442217","url":null,"abstract":"<p><p>Gene expression assays that are based on quantitative real-time PCR (qRT-PCR) method are still very popular, therefore, we developed qDATA, an open-source R-based bioinformatics application that offers a quick and intuitive analysis of raw cycle threshold (Ct) values. The application relies on a straightforward data input consisting in Ct values and on other mandatory fields specifying the experimental and control groups. qDATA automatically performs descriptive statistics, normality and statistical testing on 2<sup>-ΔCt</sup> (or ΔCt) and 2<sup>-ΔΔCt</sup> terms calculated with Livak's method. We also propose a qRT-PCR data analysis framework that depends on performing exhaustive ΔCt calculations within discrete biological replicates (BRs) and subsequently using the Livak formula for the complete sets of available data. These prerequisites arguably lead to an improved data analysis and statistical relevance. The efficiency of our computing approach was tested using input Ct values corresponding to immune related gene expression evaluated in experimental infection of <i>Drosophila melanogaster</i> and <i>Apis mellifera</i> workers. The presented results reveal that our working strategy is reliable and highlight the efficacy and performance of qDATA application.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"1-15"},"PeriodicalIF":2.2,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A domed window chamber for multi-modality optical imaging. 用于多模态光学成像的圆顶窗室。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-11-01 Epub Date: 2025-01-01 DOI: 10.1080/07366205.2024.2445452
Photini Rice, Makenna Aitken, Hasina Shir, Ricky Cordova, Jenna Montague, Dustin Tran, Urs Utzinger, Leilei Peng, Ghassan Mouneimne, Jennifer Barton
{"title":"A domed window chamber for multi-modality optical imaging.","authors":"Photini Rice, Makenna Aitken, Hasina Shir, Ricky Cordova, Jenna Montague, Dustin Tran, Urs Utzinger, Leilei Peng, Ghassan Mouneimne, Jennifer Barton","doi":"10.1080/07366205.2024.2445452","DOIUrl":"10.1080/07366205.2024.2445452","url":null,"abstract":"<p><p>Current dorsal skin flap window chambers with flat glass windows are compatible with optical coherence tomography (OCT) and multiphoton microscopy (MPM) imaging. However, light sheet fluorescence microscopy (LSFM) performs best with a cylindrical or spherical sample located between its two 90° objectives and when all sample materials have the same index of refraction (<i>n</i>). A modified window chamber with a domed viewing window made from fluorinated ethylene propylene (FEP), with n similar to water and tissue, was designed. <i>In vitro</i> imaging of collagen gels and microsphere phantoms with and without the dome showed small decreases in signal strength and image resolution due to the dome. Using a custom mouse platform for stabilization and anesthesia support, <i>in vivo</i> multimodality imaging with OCT, MPM, and LSFI was demonstrated.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"535-545"},"PeriodicalIF":2.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142913813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Characterization of nuclear microsatellites in Marchantia polymorpha (liverwort) with additional trans-specific analyses. 多态地茅（Marchantia polymorpha, liverwort）核微卫星的特征与额外的跨特异性分析。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-11-01 Epub Date: 2024-12-25 DOI: 10.1080/07366205.2024.2445454
Nicole Rodriguez Ortiz, Niharika Sharma, Tian-Xiong Zheng, James J Campanella
{"title":"Characterization of nuclear microsatellites in <i>Marchantia polymorpha</i> (liverwort) with additional trans-specific analyses.","authors":"Nicole Rodriguez Ortiz, Niharika Sharma, Tian-Xiong Zheng, James J Campanella","doi":"10.1080/07366205.2024.2445454","DOIUrl":"10.1080/07366205.2024.2445454","url":null,"abstract":"<p><p>Microsatellites are present in mitochondria, chloroplast, and nuclear DNA, but nuclear microsatellites are more useful genetic tools than those in plastids or mitochondria. Plastid and mitochondrial microsatellites have been identified in the model plant <i>Marchantia polymorpha</i> (liverwort), but no laboratory has published information on nuclear microsatellite loci. The aim of this study was to detect novel nuclear markers in the most commonly employed liverwort species, design PCR primers that would allow amplification, and characterize the subsequently generated loci. We detected 18 polymorphic nuclear loci in <i>M. polymorpha</i>, amplifiable by PCR across all chromosomes. Additionally, trans-specific amplification of the eighteen loci was characterized in the closely related taxa <i>Marchantia emarginata</i> and <i>Marchantia paleacea</i>. All loci were present in <i>M. paleacea</i>, whereas 17 of 18 primer pairs were amplified in <i>M. emarginata</i>.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"527-534"},"PeriodicalIF":2.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142891802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Development of a human tyrosinase activity inhibition assay using human melanoma cell lysate. 利用人黑色素瘤细胞裂解液建立人酪氨酸酶活性抑制试验。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-11-01 Epub Date: 2024-12-16 DOI: 10.1080/07366205.2024.2441637
Gengxuan Shi, Yunjiang Feng, Kathryn F Tonissen
{"title":"Development of a human tyrosinase activity inhibition assay using human melanoma cell lysate.","authors":"Gengxuan Shi, Yunjiang Feng, Kathryn F Tonissen","doi":"10.1080/07366205.2024.2441637","DOIUrl":"10.1080/07366205.2024.2441637","url":null,"abstract":"<p><p>Tyrosinase (TYR) inhibitors are required to treat skin hyperpigmentation. Currently live cell-based TYR assays and mushroom TYR <i>in vitro</i> assays are the common methods used to screen for TYR inhibitors. However, these methods are either time consuming and expensive or are not human TYR (<i>hs</i>TYR) specific. Here, we describe a simple <i>hs</i>TYR assay using cell lysate prepared from pigmented human melanoma cell lines that takes less than 3 hours to complete after collecting cell pellets. We confirmed the assay is species specific by using a known <i>hs</i>TYR inhibitor, kojic acid, as a positive control, while arbutin, which inhibits mushroom TYR, but not <i>hs</i>TYR, was not effective. This assay is a simple method to confirm <i>hs</i>TYR inhibition before conducting follow-up studies in live biological models.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"547-551"},"PeriodicalIF":2.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142827092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Who wants to live forever? Models shaping the future of aging research. 谁想长生不老？塑造老龄化研究未来的模型。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-11-01 Epub Date: 2025-01-06 DOI: 10.1080/07366205.2024.2445467
Annie Coulson
{"title":"Who wants to live forever? Models shaping the future of aging research.","authors":"Annie Coulson","doi":"10.1080/07366205.2024.2445467","DOIUrl":"10.1080/07366205.2024.2445467","url":null,"abstract":"","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"523-526"},"PeriodicalIF":2.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Optimized for routine: highly sensitive fluorescent Telomeric Repeat Amplification Protocol (f-TRAP). 常规优化：高灵敏度荧光端粒重复扩增协议（f-TRAP）。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-10-01 Epub Date: 2024-12-15 DOI: 10.1080/07366205.2024.2432805
Silke Fähnrich, Anne Wedemann, Laura Steenpass, Wilhelm Gerhard Dirks
{"title":"Optimized for routine: highly sensitive fluorescent Telomeric Repeat Amplification Protocol (f-TRAP).","authors":"Silke Fähnrich, Anne Wedemann, Laura Steenpass, Wilhelm Gerhard Dirks","doi":"10.1080/07366205.2024.2432805","DOIUrl":"10.1080/07366205.2024.2432805","url":null,"abstract":"<p><p>The strict suppression of telomerase activity (TA) in terminally differentiated human cells causes a shortening of the chromosome ends after each cell division. This tumor suppression surveillance mechanism is associated with a limited number of cell divisions known as Hayflick limit. Here we present an optimized protocol for measuring TA that combines a fluorescently labeled bait primer and polymerase chain reaction (PCR) amplification with analytical capillary electrophoresis (CE) to achieve a detection limit of one telomerase-positive cell per ten thousand negative cells. In research laboratories today, a broad panel of TRAP assay protocols enables the assessment of the immortality of newly generated cell lines or the unambiguous evaluation of the reprogramming of induced pluripotent stem cells (iPSCs). The present f-TRAP protocol, optimized for routine use, enables fast ad hoc application for single measurements up to a high throughput of mass samples using a triplicate approach of different lysate concentrations. Final CE analysis facilitates standardized data processing and storage for documentation of results and could make f-TRAP a useful assay in research and clinical oncology.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"517-522"},"PeriodicalIF":2.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142827093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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