发布求助
文献互助 智能选刊 最新文献

BioTechniques最新文献

筛选
英文 中文
Comparing robotic and manual injection methods in zebrafish embryos for high-throughput RNA silencing using CRISPR-RfxCas13d. 比较使用 CRISPR-RfxCas13d 在斑马鱼胚胎中进行高通量 RNA 沉默的机器人和人工注射方法。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-05-01 Epub Date: 2024-02-29 DOI: 10.2144/btn-2023-0062
Joaquin Abugattas-Nuñez Del Prado, Yi Ding, Jan de Sonneville, Kees-Jan van der Kolk, Miguel A Moreno-Mateos, Edward Málaga-Trillo, Herman P Spaink
{"title":"Comparing robotic and manual injection methods in zebrafish embryos for high-throughput RNA silencing using CRISPR-RfxCas13d.","authors":"Joaquin Abugattas-Nuñez Del Prado, Yi Ding, Jan de Sonneville, Kees-Jan van der Kolk, Miguel A Moreno-Mateos, Edward Málaga-Trillo, Herman P Spaink","doi":"10.2144/btn-2023-0062","DOIUrl":"10.2144/btn-2023-0062","url":null,"abstract":"<p><p>In this study, the authors compared the efficiency of automated robotic and manual injection methods for the CRISPR-RfxCas13d (CasRx) system for mRNA knockdown and Cas9-mediated DNA targeting in zebrafish embryos. They targeted the no tail (<i>TBXTA</i>) gene as a proof-of-principle, evaluating the induced embryonic phenotypes. Both Cas9 and CasRx systems caused loss of function phenotypes for <i>TBXTA</i>. Cas9 protein exhibited a higher percentage of severe phenotypes compared with mRNA, while CasRx protein and mRNA showed similar efficiency. Both robotic and manual injections demonstrated comparable phenotype percentages and mortality rates. The findings highlight the potential of RNA-targeting CRISPR effectors for precise gene knockdown and endorse automated microinjection at a speed of 1.0 s per embryo as a high-throughput alternative to manual methods.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139989247","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
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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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
'Gel-Stacks' gently confine or reversibly immobilize arrays of single DNA molecules for manipulation and study. 凝胶堆栈 "可轻柔地限制或可逆地固定单个 DNA 分子阵列，以便进行操作和研究。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-04-24 DOI: 10.2144/btn-2023-0123
Susana Calle-Casteñeda, Eamon Winden, Alejandro Vasquez-Echeverri, Matthew Schickling, Evelyn Browning, Juan Pablo Hernandez Ortiz, David C Schwartz
{"title":"'Gel-Stacks' gently confine or reversibly immobilize arrays of single DNA molecules for manipulation and study.","authors":"Susana Calle-Casteñeda, Eamon Winden, Alejandro Vasquez-Echeverri, Matthew Schickling, Evelyn Browning, Juan Pablo Hernandez Ortiz, David C Schwartz","doi":"10.2144/btn-2023-0123","DOIUrl":"https://doi.org/10.2144/btn-2023-0123","url":null,"abstract":"Large DNA molecules (>20 kb) are difficult analytes prone to breakage during serial manipulations and cannot be 'rescued' as full-length amplicons. Accordingly, to present, modify and analyze arrays of large, single DNA molecules, we created an easily realizable approach offering gentle confinement conditions or immobilization via spermidine condensation for controlled delivery of reagents that support live imaging by epifluorescence microscopy termed 'Gel-Stacks.' Molecules are locally confined between two hydrogel surfaces without covalent tethering to support time-lapse imaging and multistep workflows that accommodate large DNA molecules. With a thin polyacrylamide gel layer covalently bound to a glass surface as the base and swappable, reagent-infused, agarose slabs on top, DNA molecules are stably presented for imaging during reagent delivery by passive diffusion.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140661585","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
Rectal swab DNA collection protocol for PCR genotyping in rats. 用于大鼠 PCR 基因分型的直肠拭子 DNA 采集方案。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-04-23 DOI: 10.2144/btn-2024-0023
Audrey E. Kaye, Jacob W. Proctor-Bonbright, Jai Y. Yu
{"title":"Rectal swab DNA collection protocol for PCR genotyping in rats.","authors":"Audrey E. Kaye, Jacob W. Proctor-Bonbright, Jai Y. Yu","doi":"10.2144/btn-2024-0023","DOIUrl":"https://doi.org/10.2144/btn-2024-0023","url":null,"abstract":"DNA collection is essential for genotyping laboratory animals. Common collection methods require tissue amputation, causing discomfort and injury. Rectal swabbing has been proposed as an effective, minimally invasive alternative, but an evidence-backed protocol for the technique remains unavailable. This report evaluates the effects of collection parameters on the quality of PCR results and presents a protocol for genotyping a litter of rats within 3-5 h. Samples with 2-8 scrapes produced enough DNA to amplify targets up to ∼1800 bp long using PCR. Rectal swabbing produced PCR results with similar utility as ear clip samples, and results were unaffected by residual fecal matter or cell debris. The protocol enables fast, minimally invasive and repeatable genotyping using commercial PCR reagents.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140672344","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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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
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":null,"pages":null},"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
首页 上一页 下一页 尾页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们：info@booksci.cn Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：481959085
Book学术官方微信