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Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples. 比较和优化古代 DNA 样本的方案和全基因组捕获条件。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-05-01 Epub Date: 2024-03-26 DOI: 10.2144/btn-2023-0107
Reyhan Yaka, Maja Krzewińska, Vendela Kempe Lagerholm, Anna Linderholm, Füsun Özer, Mehmet Somel, Anders Götherström
{"title":"Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples.","authors":"Reyhan Yaka, Maja Krzewińska, Vendela Kempe Lagerholm, Anna Linderholm, Füsun Özer, Mehmet Somel, Anders Götherström","doi":"10.2144/btn-2023-0107","DOIUrl":"10.2144/btn-2023-0107","url":null,"abstract":"<p><p>Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"216-223"},"PeriodicalIF":2.7,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140288161","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 free and user-friendly software protocol for the quantification of microfauna swimming behavior. 用于量化微型动物游泳行为的免费且用户友好的软件协议。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-05-01 Epub Date: 2024-02-29 DOI: 10.2144/btn-2024-0001
Colleen M McMaken, Kristin E Gribble
{"title":"A free and user-friendly software protocol for the quantification of microfauna swimming behavior.","authors":"Colleen M McMaken, Kristin E Gribble","doi":"10.2144/btn-2024-0001","DOIUrl":"10.2144/btn-2024-0001","url":null,"abstract":"<p><p>Characterizing swimming behavior can provide a holistic assessment of the health, physiology and ecology of microfaunal species when done in conjunction with measuring other biological parameters. However, tracking and quantifying microfauna swimming behavior using existing automated tools is often difficult due to the animals' small size or transparency, or because of the high cost, expertise, or labor needed for the analysis. To address these issues, we created a cost-effective, user-friendly protocol for behavior analysis that employs the free software packages HitFilm and ToxTrac along with the R package 'trajr' and used the method to quantify the behavior of rotifers. This protocol can be used for other microfaunal species for which investigators may face similar issues in obtaining measurements of swimming behavior.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"174-182"},"PeriodicalIF":2.2,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11416747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139995521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Isolation and characterization of Paenibacillus peoriae JC-3jx from Dendrobium nobile. 从金钗石斛中分离并鉴定 peoriae JC-3jx Paenibacillus。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-05-01 Epub Date: 2024-03-12 DOI: 10.2144/btn-2023-0083
ZhiPing Li, Yuan Lin, FeiFei Song, RuoNan Zheng, QinGeng Huang
{"title":"Isolation and characterization of <i>Paenibacillus peoriae</i> JC-3jx from <i>Dendrobium nobile</i>.","authors":"ZhiPing Li, Yuan Lin, FeiFei Song, RuoNan Zheng, QinGeng Huang","doi":"10.2144/btn-2023-0083","DOIUrl":"10.2144/btn-2023-0083","url":null,"abstract":"<p><p><i>Dendrobium</i> is a rich source of high-value natural components. Endophytic fungi are well studied, yet bacteria research is limited. In this study, endophytic bacteria from <i>Dendrobium nobile</i> were isolated using an improved method, showing inhibition of pathogens and growth promotion. JC-3jx, identified as <i>Paenibacillus peoriae</i>, exhibited significant inhibitory activity against tested fungi and bacteria, including <i>Escherichia coli</i>. JC-3jx also promoted corn seed rooting and <i>Dendrobium</i> growth, highlighting its excellent biocontrol and growth-promoting potential.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"192-202"},"PeriodicalIF":2.7,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140101017","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
Extraterrestrial agriculture: plant cultivation in space. 地外农业：太空植物栽培。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-04-11 DOI: 10.2144/btn-2024-0033
Beatrice Bowlby
{"title":"Extraterrestrial agriculture: plant cultivation in space.","authors":"Beatrice Bowlby","doi":"10.2144/btn-2024-0033","DOIUrl":"https://doi.org/10.2144/btn-2024-0033","url":null,"abstract":"[Formula: see text] Researchers are using various techniques and technologies to study how plants grow in extraterrestrial conditions with the hopes of sustaining longer missions for exploring deep space as well as being able to one day cultivate crops on other planets.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"60 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140571236","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 and evaluation of a single-tube nested PCR with colorimetric assay for Mycobacterium tuberculosis detection. 开发和评估用于检测结核分枝杆菌的单管巢式 PCR 比色法。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-04-11 DOI: 10.2144/btn-2023-0080
Marcela Pereira Salazar, Juliana Figueiredo da Costa Lima Suassuna Monteiro, Wlisses Henrique Veloso Carvalho-Silva, George Tadeu Nunes Diniz, Roberto Pereira Werkhauser, Lílian Maria Lapa Montenegro, Haiana Charifker Schindler
{"title":"Development and evaluation of a single-tube nested PCR with colorimetric assay for Mycobacterium tuberculosis detection.","authors":"Marcela Pereira Salazar, Juliana Figueiredo da Costa Lima Suassuna Monteiro, Wlisses Henrique Veloso Carvalho-Silva, George Tadeu Nunes Diniz, Roberto Pereira Werkhauser, Lílian Maria Lapa Montenegro, Haiana Charifker Schindler","doi":"10.2144/btn-2023-0080","DOIUrl":"https://doi.org/10.2144/btn-2023-0080","url":null,"abstract":"Molecular techniques have revolutionized tuberculosis (TB) diagnosis by offering a faster and more sensitive approach, detecting <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) DNA directly from samples. Single-tube nested PCR (STNPCR) combines two PCR reactions with separate oligonucleotide sets in a single tube. Moreover, colorimetric methods in PCR products have been studied for pathogen detection. Thus, this study aimed to establish a novel system based on colorimetric STNPCR for <i>Mtb</i> detection using microtiter plates with <i>IS6110</i>-amplified fragments. The results showed a general colorimetric STNPCR detection limit of 1 pg/μl. Its general sensitivity and specificity were 76.62 and 60.53%, respectively, with kappa index agreement of 0.166.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"54 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140603201","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
Fully in vitro iterative construction of a 24 kb-long artificial DNA sequence to store digital information. 完全体外迭代构建 24 kb 长的人工 DNA 序列，用于存储数字信息。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-04-04 DOI: 10.2144/btn-2023-0109
Julien Leblanc, Olivier Boulle, Emeline Roux, Jacques Nicolas, Dominique Lavenier, Yann Audic
{"title":"Fully in vitro iterative construction of a 24 kb-long artificial DNA sequence to store digital information.","authors":"Julien Leblanc, Olivier Boulle, Emeline Roux, Jacques Nicolas, Dominique Lavenier, Yann Audic","doi":"10.2144/btn-2023-0109","DOIUrl":"https://doi.org/10.2144/btn-2023-0109","url":null,"abstract":"In the absence of a DNA template, the <i>ab initio</i> production of long double-stranded DNA molecules of predefined sequences is particularly challenging. The DNA synthesis step remains a bottleneck for many applications such as functional assessment of ancestral genes, analysis of alternative splicing or DNA-based data storage. In this report we propose a fully <i>in vitro</i> protocol to generate very long double-stranded DNA molecules starting from commercially available short DNA blocks in less than 3 days using Golden Gate assembly. This innovative application allowed us to streamline the process to produce a 24 kb-long DNA molecule storing part of <i>the</i> <i>Declaration of the Rights of Man and of the Citizen</i> of 1789 . The DNA molecule produced can be readily cloned into a suitable host/vector system for amplification and selection.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"37 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140571062","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
Considerations for developing mitochondrial transplantation techniques for individualized medicine. 开发用于个体化医疗的线粒体移植技术的考虑因素。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-04-01 Epub Date: 2024-02-29 DOI: 10.2144/btn-2023-0072
Kit Neikirk, Dominique C Stephens, Heather K Beasley, Andrea G Marshall, Jennifer A Gaddy, Steven M Damo, Antentor O Hinton
{"title":"Considerations for developing mitochondrial transplantation techniques for individualized medicine.","authors":"Kit Neikirk, Dominique C Stephens, Heather K Beasley, Andrea G Marshall, Jennifer A Gaddy, Steven M Damo, Antentor O Hinton","doi":"10.2144/btn-2023-0072","DOIUrl":"10.2144/btn-2023-0072","url":null,"abstract":"<p><p>Tweetable abstract Mitochondrial transplantation has been used to treat various diseases associated with mitochondrial dysfunction. Here, we highlight the considerations in quality control mechanisms that should be considered in the context of mitochondrial transplantation.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"125-134"},"PeriodicalIF":2.7,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139989248","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
An industry perspective approach and control strategy for implementation of ready-to-use cells in bioassays: survey outcome and recommendations. 在生物测定中使用即用型细胞的行业视角方法和控制策略：调查结果和建议。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-04-01 Epub Date: 2024-02-09 DOI: 10.2144/btn-2023-0086
John R White, Sammina Ahmed, Jan Amstrup, Petra Bennington, Zhijie Jey Cheng, Peter Day, Keneshia K Haenssen, Adi Kozminsky-Atias, Eva Martinez, Esther Hq Ong, Isam Qahwash, Elaine Se Stokes, Jenny Wang
{"title":"An industry perspective approach and control strategy for implementation of ready-to-use cells in bioassays: survey outcome and recommendations.","authors":"John R White, Sammina Ahmed, Jan Amstrup, Petra Bennington, Zhijie Jey Cheng, Peter Day, Keneshia K Haenssen, Adi Kozminsky-Atias, Eva Martinez, Esther Hq Ong, Isam Qahwash, Elaine Se Stokes, Jenny Wang","doi":"10.2144/btn-2023-0086","DOIUrl":"10.2144/btn-2023-0086","url":null,"abstract":"<p><p>The BioPhorum Development Group is an industry collaboration enabling the sharing of common practices for the development of biopharmaceuticals. Bioassays are an important part of an analytical control system. Utilization of ready-to-use cells can increase operational flexibility and improve efficiency by providing frozen cell banks uniform stock while removing challenges associated with maintaining cultured cells. The BioPhorum Development Group-Bioassay workstream conducted an intercompany benchmarking survey and group discussions around the use of ready-to-use cells for bioassays. The results of the collaboration provide alignment on nomenclature, production, qualification and implementation of ready-to-use cells to support the assay life cycle.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"135-144"},"PeriodicalIF":2.7,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139705986","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
High-throughput screening for a SARS-CoV-2 frameshifting inhibitor using a cell-free protein synthesis system. 利用无细胞蛋白质合成系统高通量筛选 SARS-CoV-2 换帧抑制剂。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-04-01 Epub Date: 2024-01-31 DOI: 10.2144/btn-2023-0102
Kodai Machida, Rin Tanaka, Seraya Miki, Shotaro Noseda, Mayumi Yuasa-Sunagawa, Hiroaki Imataka
{"title":"High-throughput screening for a SARS-CoV-2 frameshifting inhibitor using a cell-free protein synthesis system.","authors":"Kodai Machida, Rin Tanaka, Seraya Miki, Shotaro Noseda, Mayumi Yuasa-Sunagawa, Hiroaki Imataka","doi":"10.2144/btn-2023-0102","DOIUrl":"10.2144/btn-2023-0102","url":null,"abstract":"<p><p>Programmed-1 ribosomal frameshifting (-1 PRF) is a translational mechanism adopted by some viruses, including SARS-CoV-2. To find a compound that can inhibit -1 PRF in SARS-CoV-2, we set up a high-throughput screening system using a HeLa cell extract-derived cell-free protein synthesis (CFPS) system. A total of 32,000 compounds were individually incubated with the CFPS system programmed with a -1 PRF-EGFP template. Several compounds were observed to decrease the -1 PRF-driven fluorescence, and one of them had some suppressive effect on -1 PRF of a SARS-CoV-2 genome sequence in transfected cells. Thus the CFPS system can be used as a tool for a high-throughput screening of chemicals.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"161-168"},"PeriodicalIF":2.7,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139641560","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
Multiparameter screen optimizes immunoprecipitation. 多参数筛选可优化免疫沉淀。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-04-01 Epub Date: 2024-02-29 DOI: 10.2144/btn-2023-0051
Shaoshuai Xie, Leila Saba, Hua Jiang, Omar R Bringas, Mehrnoosh Oghbaie, Luciano Di Stefano, Vadim Sherman, John LaCava
{"title":"Multiparameter screen optimizes immunoprecipitation.","authors":"Shaoshuai Xie, Leila Saba, Hua Jiang, Omar R Bringas, Mehrnoosh Oghbaie, Luciano Di Stefano, Vadim Sherman, John LaCava","doi":"10.2144/btn-2023-0051","DOIUrl":"10.2144/btn-2023-0051","url":null,"abstract":"<p><p>Immunoprecipitation (IP) coupled with mass spectrometry effectively maps protein-protein interactions when genome-wide, affinity-tagged cell collections are used. Such studies have recorded significant portions of the compositions of physiological protein complexes, providing draft 'interactomes'; yet many constituents of protein complexes still remain uncharted. This gap exists partly because high-throughput approaches cannot optimize each IP. A key challenge for IP optimization is stabilizing <i>in vivo</i> interactions during the transfer from cells to test tubes; failure to do so leads to the loss of genuine interactions during the IP and subsequent failure to detect. Our high-content screening method explores the relationship between <i>in vitro</i> chemical conditions and IP outcomes, enabling rapid empirical optimization of conditions for capturing target macromolecular assemblies.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"145-152"},"PeriodicalIF":2.7,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11091867/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139995522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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