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Uncovering the molecular mechanisms behind Alzheimer's and Parkinson's disease through multi-omics: an interview with Bruno A. Benitez. 通过多组学揭示阿尔茨海默病和帕金森病背后的分子机制：采访布鲁诺·a·贝尼特斯。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2025-01-01 Epub Date: 2025-01-31 DOI: 10.1080/07366205.2025.2457900
Bruno A Benitez
{"title":"Uncovering the molecular mechanisms behind Alzheimer's and Parkinson's disease through multi-omics: an interview with Bruno A. Benitez.","authors":"Bruno A Benitez","doi":"10.1080/07366205.2025.2457900","DOIUrl":"10.1080/07366205.2025.2457900","url":null,"abstract":"","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"5-8"},"PeriodicalIF":2.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063427","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 : 2025-01-01 Epub 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":"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":"9-22"},"PeriodicalIF":2.2,"publicationDate":"2025-01-01","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
Efficient production system for hydrogel-based transparent soil for plant root observation. 植物根系观察用透明水凝胶土高效生产系统。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2025-01-01 Epub Date: 2025-01-31 DOI: 10.1080/07366205.2025.2457892
Naoyuki Sotta, Wenhao Li, Toru Fujiwara
{"title":"Efficient production system for hydrogel-based transparent soil for plant root observation.","authors":"Naoyuki Sotta, Wenhao Li, Toru Fujiwara","doi":"10.1080/07366205.2025.2457892","DOIUrl":"10.1080/07366205.2025.2457892","url":null,"abstract":"<p><p>Observation of plant root morphology in soil is of fundamental importance in plant research, but the lack of transparency of the soil hampers direct observation of roots. One of the approaches to overcome this technical limitation is the use of \"transparent soil\" (TS), hydrogel-based beads produced by spherification of gelling agents. However, the production of TS by natural dripping of gelling solution can be labor intensive, time consuming and difficult to maintain consistent product quality. Here we present a semi-automated system for TS production. A three-channel peristatic pump controls the critical parameters for spherification, such as drop height and ionic strength, allowing larger-scale TS production with less manual operation. This system improves the efficiency of experiments using TS and enables large-scale experiments requiring large amounts of TS.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"35-39"},"PeriodicalIF":2.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063425","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
RNA extraction and RNA-sequencing method for transcriptomic analysis of Mycobacterium tuberculosis. 结核分枝杆菌转录组学分析的RNA提取和RNA测序方法。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2025-01-01 Epub Date: 2025-02-16 DOI: 10.1080/07366205.2025.2457887
Morgan R Hiebert, Meenu K Sharma, Alwyn Go, Christine Bonner, Vanessa Laminman, Morag Graham, Hafid Soualhine
{"title":"RNA extraction and RNA-sequencing method for transcriptomic analysis of <i>Mycobacterium tuberculosis</i>.","authors":"Morgan R Hiebert, Meenu K Sharma, Alwyn Go, Christine Bonner, Vanessa Laminman, Morag Graham, Hafid Soualhine","doi":"10.1080/07366205.2025.2457887","DOIUrl":"10.1080/07366205.2025.2457887","url":null,"abstract":"<p><p>RNA-sequencing (RNA-seq) technologies have advanced exponentially in recent years, however, the application of RNA-seq to <i>Mycobacterium tuberculosis</i> remains limited. We present a wet-lab and computational protocol for RNA-seq based transcriptomics that was tested on 12 replicates each of 11 clinical isolates of <i>M. tuberculosis</i> (<i>n</i> = 132) grown <i>in vitro</i> with and without pyrazinamide exposure. This RNA extraction method uses low-volume cultures, mechanical lysis, TRIzol<sup>™</sup> phase separation, and column-based purification to produce high yields of pure, intact RNA followed by rRNA depletion and cDNA library preparation. The detection of unique transcripts was optimized at a sequencing depth of 15 million reads. This method detected differential RNA expression in experimental sets with and without pyrazinamide exposure, demonstrating that the method is suitable for RNA-seq applications.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"23-34"},"PeriodicalIF":2.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143432315","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
CRISPR screens in neurological research: exploring the functional basis of aging and disease. 神经学研究中的CRISPR筛选：探索衰老和疾病的功能基础。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2025-01-01 Epub Date: 2025-02-03 DOI: 10.1080/07366205.2025.2457889
Jenny Straiton
{"title":"CRISPR screens in neurological research: exploring the functional basis of aging and disease.","authors":"Jenny Straiton","doi":"10.1080/07366205.2025.2457889","DOIUrl":"10.1080/07366205.2025.2457889","url":null,"abstract":"","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"1-4"},"PeriodicalIF":2.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078559","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 : 2024-12-01 Epub 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":"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":"581-591"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","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
UK Biobank: what can it do, how you can use it and how is it being used? 英国生物银行：它能做什么，你如何使用它，它是如何被使用的？
IF 2.5 4区 工程技术
BioTechniques Pub Date : 2024-12-01 Epub 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":"10.1080/07366205.2024.2441639","url":null,"abstract":"","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"553-557"},"PeriodicalIF":2.5,"publicationDate":"2024-12-01","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
Developing advanced organoids: challenges, progress, and outlook. 发展先进类器官：挑战、进展与展望。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-12-01 Epub Date: 2025-01-29 DOI: 10.1080/07366205.2024.2442825
Oscar J Abilez
{"title":"Developing advanced organoids: challenges, progress, and outlook.","authors":"Oscar J Abilez","doi":"10.1080/07366205.2024.2442825","DOIUrl":"10.1080/07366205.2024.2442825","url":null,"abstract":"","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"575-580"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057885","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 : 2024-12-01 Epub 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":"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":"559-573"},"PeriodicalIF":2.2,"publicationDate":"2024-12-01","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
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