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Alkaline dip DNA extraction from skin mucus for high-throughput sexing of sterlets (Acipenser ruthenus).
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2025-02-20 DOI: 10.1080/07366205.2025.2467584
Ryuhei Kinami, Toshinao Ineno
{"title":"Alkaline dip DNA extraction from skin mucus for high-throughput sexing of sterlets (<i>Acipenser ruthenus</i>).","authors":"Ryuhei Kinami, Toshinao Ineno","doi":"10.1080/07366205.2025.2467584","DOIUrl":"https://doi.org/10.1080/07366205.2025.2467584","url":null,"abstract":"<p><p>Studies on simple DNA extraction methods from fish mucus, which is an ideal resource for noninvasive sampling, are scarce. In the aquaculture of sturgeons such as sterlets (<i>Acipenser ruthenus</i>), a high-throughput genetic sexing method is needed, as only females are reared to maturity for their roe. Here, DNA extraction methods using HotSHOT (hot sodium hydroxide and tris), a novel alkaline dip, alkaline glycol, and water were compared using the skin mucus of sterlets (n = 8) collected with a toothpick. High-throughput sexing of sterlets from six production batches (n = 3953) was also evaluated using HotSHOT or alkaline dip. An alkaline dip with 10-25 mM NaOH was an effective alternative to HotSHOT, eliminating the heating and neutralizing steps. Regarding high-throughput sexing, > 99% (3946) individuals were successfully genotyped on the first PCR trial, and genotype ratios of each batch were close to 1:1, showing applicability of the alkaline dip method for practical sterlet sexing.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"1-10"},"PeriodicalIF":2.2,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466823","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 an enhanced anti-pan-N-formylmethionine-specific antibody.
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2025-02-20 DOI: 10.1080/07366205.2025.2467583
Dasom Kim, Kyu-Sang Park, Cheol-Sang Hwang
{"title":"Development of an enhanced anti-pan-N-formylmethionine-specific antibody.","authors":"Dasom Kim, Kyu-Sang Park, Cheol-Sang Hwang","doi":"10.1080/07366205.2025.2467583","DOIUrl":"https://doi.org/10.1080/07366205.2025.2467583","url":null,"abstract":"<p><p>Both bacterial and eukaryotic ribosomes can initiate protein synthesis with formylmethionine (fMet), but detecting fMet-bearing peptides and fMet-bearing proteins has been challenging due to the lack of effective anti-pan-fMet antibodies. Previously, we developed a polyclonal anti-fMet antibody using a fMet-Gly-Ser-Gly-Cys pentapeptide that detects those fMet-bearing peptides and fMet-bearing proteins regardless of their sequence context. In this study, we significantly improved the antibody's specificity and affinity by using a mixture of fMet-Xaa-Cys tripeptides (Xaa, any of the 20 amino acids) as the immunogen. This newly optimized anti-fMet antibody is a powerful, cost-effective tool for detecting fMet-bearing proteins across species. Furthermore, this approach provides a foundation for developing anti-pan-specific antibodies targeting other N-terminal modifications through acylation, alkylation, oxidation, arginylation, etc.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"1-10"},"PeriodicalIF":2.2,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456607","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
Uncovering the molecular mechanisms behind Alzheimer's and Parkinson's disease through multi-omics: an interview with Bruno A. Benitez.
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.
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
CRISPR screens in neurological research: exploring the functional basis of aging and disease.
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
RNA extraction and RNA-sequencing method for transcriptomic analysis of Mycobacterium tuberculosis.
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
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
Developing advanced organoids: challenges, progress, and outlook.
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
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