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MSCProfiler: a single cell image processing workflow to investigate mesenchymal stem cell heterogeneity. MSCProfiler：用于研究间充质干细胞异质性的单细胞图像处理工作流程。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2023-11-01 Epub Date: 2023-11-02 DOI: 10.2144/btn-2023-0048
Ayona Gupta, Safia Kousar Shaik, Lakshmi Balasubramanian, Uttara Chakraborty
{"title":"MSCProfiler: a single cell image processing workflow to investigate mesenchymal stem cell heterogeneity.","authors":"Ayona Gupta, Safia Kousar Shaik, Lakshmi Balasubramanian, Uttara Chakraborty","doi":"10.2144/btn-2023-0048","DOIUrl":"10.2144/btn-2023-0048","url":null,"abstract":"<p><p>Single cell cytometry has demonstrated plausible immuno-heterogeneity of mesenchymal stem cells (MSCs) owing to their multivariate stromal origin. To contribute successfully to next-generation stem cell therapeutics, a deeper understanding of their cellular morphology and immunophenotype is important. In this study, the authors describe MSCProfiler, an image analysis pipeline developed using CellProfiler software. This workflow can extract geometrical and texture features such as shape, size, eccentricity and entropy, along with intensity values of the surface markers from multiple single cell images obtained using imaging flow cytometry. This screening pipeline can be used to analyze geometrical and texture features of all types of MSCs across different passages hallmarked by enhanced feature extraction potential from brightfield and fluorescent images of the cells.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"195-209"},"PeriodicalIF":2.7,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71420364","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
Colorimetric analysis of C-reactive protein via 'jellyfish' probe-based exonuclease III-assisted multiple-signal recycles. 通过基于“水母”探针的核酸外切酶III辅助多种信号回收的C反应蛋白比色分析。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2023-10-01 Epub Date: 2023-08-24 DOI: 10.2144/btn-2023-0018
Jinghui An, Huajun Wang, Tong Su, Fengwu Shi, Su Liu
{"title":"Colorimetric analysis of C-reactive protein via 'jellyfish' probe-based exonuclease III-assisted multiple-signal recycles.","authors":"Jinghui An,&nbsp;Huajun Wang,&nbsp;Tong Su,&nbsp;Fengwu Shi,&nbsp;Su Liu","doi":"10.2144/btn-2023-0018","DOIUrl":"10.2144/btn-2023-0018","url":null,"abstract":"<p><p>C-reactive protein (CRP) is a potential biomarker for evaluating inflammatory responses in patients receiving coronary artery bypass graft surgery. Here, the authors depict a sensitive and reliable colorimetric approach for CRP analysis. In this method, an aptamer specifically binds with CRP and an initiator sequence is released from an arch probe to activate signal amplification. The released initiator sequence hybridizes with the toehold section in the 'jellyfish' probe to form a blunt terminus to induce exonuclease III-assisted signal amplification. The method exhibited a low limit of detection of 1.32 ng/ml and high intraday and interday precision for CRP detection. In summary, this colorimetric approach may provide a potential alternative tool for the evaluation of inflammation in patients receiving coronary artery bypass graft and clinical diagnostics of disease.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"143-149"},"PeriodicalIF":2.7,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10059650","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 cell hybridization-based method of generating recombinant rabbit monoclonal antibodies for detecting cytokines. 一种基于细胞杂交的产生用于检测细胞因子的重组兔单克隆抗体的方法。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2023-10-01 Epub Date: 2023-09-06 DOI: 10.2144/btn-2023-0026
Yu Peng, Chun'e Zhang, Minyan Deng, Haijuan Jiang, Huishu Huang, Yue Li, Weiping Lai, Yu-Pin Lin, Jun Yu
{"title":"A cell hybridization-based method of generating recombinant rabbit monoclonal antibodies for detecting cytokines.","authors":"Yu Peng,&nbsp;Chun'e Zhang,&nbsp;Minyan Deng,&nbsp;Haijuan Jiang,&nbsp;Huishu Huang,&nbsp;Yue Li,&nbsp;Weiping Lai,&nbsp;Yu-Pin Lin,&nbsp;Jun Yu","doi":"10.2144/btn-2023-0026","DOIUrl":"10.2144/btn-2023-0026","url":null,"abstract":"<p><p>Recombinant rabbit monoclonal antibodies (rabbit rAbs) have shown promise in various biomedical fields. However, it is challenging and costly to generate rabbit rAbs using traditional techniques. Here we describe a convenient and cost-effective method. Using this method, we generated rabbit rAbs against mouse soluble IL-6 receptor α with affinities in the range of 10<sup>-9</sup> to 10<sup>-12</sup> M. The presented method is suitable for industrial and academic scientists looking to customize rabbit rAbs for their research.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"150-156"},"PeriodicalIF":2.7,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10164919","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
Microbial forensics: what we've learned from Amerithrax and beyond. 微生物取证：我们从Ameritrax和其他方面学到了什么。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2023-10-01 Epub Date: 2023-10-06 DOI: 10.2144/btn-2023-0084
Louis Gautier
{"title":"Microbial forensics: what we've learned from Amerithrax and beyond.","authors":"Louis Gautier","doi":"10.2144/btn-2023-0084","DOIUrl":"10.2144/btn-2023-0084","url":null,"abstract":"<p><p>The Amerithrax investigation into anthrax letter attacks in the USA forever changed the game in microbial forensics. Here we review the techniques used, then and now, to neutralize bioterrorism threats. [Formula: see text].</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"129-132"},"PeriodicalIF":2.2,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41102348","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
PlayBack cloning: simple, reversible, cost-effective cloning for the combinatorial assembly of complex expression constructs. 回放克隆：简单、可逆、经济高效的克隆，用于复杂表达构建体的组合组装。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2023-10-01 Epub Date: 2023-10-10 DOI: 10.2144/btn-2023-0042
Gregory Foran, Ryan D Hallam, Marvel Megaly, Anel Turgambayeva, Aleksandar Necakov
{"title":"PlayBack cloning: simple, reversible, cost-effective cloning for the combinatorial assembly of complex expression constructs.","authors":"Gregory Foran, Ryan D Hallam, Marvel Megaly, Anel Turgambayeva, Aleksandar Necakov","doi":"10.2144/btn-2023-0042","DOIUrl":"10.2144/btn-2023-0042","url":null,"abstract":"<p><p>With advancements in multicomponent molecular biological tools, the need for versatile, rapid and cost-effective cloning that enables successful combinatorial assembly of DNA plasmids of interest is becoming increasingly important. Unfortunately, current cloning platforms fall short regarding affordability, ease of combinatorial assembly and, above all, the ability to iteratively remove individual cassettes at will. Herein we construct, implement and make available a broad set of cloning vectors, called PlayBack vectors, that allow for the expression of several different constructs simultaneously under separate promoters. Overall, this system is substantially cheaper than other multicomponent cloning systems, has usability for a wide breadth of experimental paradigms and includes the novel feature of being able to selectively remove components of interest at will at any stage of the cloning platform.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"168-178"},"PeriodicalIF":2.7,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41181906","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
Single-cell RNA sequencing of bronchoscopy specimens: development of a rapid minimal handling protocol. 支气管镜标本的单细胞RNA测序：快速最小处理方案的开发。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2023-10-01 Epub Date: 2023-10-10 DOI: 10.2144/btn-2023-0017
Firoozeh V Gerayeli, Stephen Milne, Chen Xi Yang, Xuan Li, Elizabeth Guinto, Julia Shun-Wei Yang, Chung Yan Cheung, Tara R Stach, Tawimas Shaipanich, Janice M Leung, Don D Sin
{"title":"Single-cell RNA sequencing of bronchoscopy specimens: development of a rapid minimal handling protocol.","authors":"Firoozeh V Gerayeli, Stephen Milne, Chen Xi Yang, Xuan Li, Elizabeth Guinto, Julia Shun-Wei Yang, Chung Yan Cheung, Tara R Stach, Tawimas Shaipanich, Janice M Leung, Don D Sin","doi":"10.2144/btn-2023-0017","DOIUrl":"10.2144/btn-2023-0017","url":null,"abstract":"<p><p>Single-cell RNA sequencing (scRNA-seq) is an important tool for understanding disease pathophysiology, including airway diseases. Currently, the majority of scRNA-seq studies in airway diseases have used invasive methods (airway biopsy, surgical resection), which carry inherent risks and thus present a major limitation to scRNA-seq investigation of airway pathobiology. Bronchial brushing, where the airway mucosa is sampled using a cytological brush, is a viable, less invasive method of obtaining airway cells for scRNA-seq. Here we describe the development of a rapid and minimal handling protocol for preparing single-cell suspensions from bronchial brush specimens for scRNA-seq. Our optimized protocol maximizes cell recovery and cell quality and facilitates large-scale profiling of the airway transcriptome at single-cell resolution.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"157-167"},"PeriodicalIF":2.7,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41181907","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
Quantitative analysis of lncRNA in formalin-fixed paraffin-embedded tissues of oral squamous cell carcinoma. 口腔鳞状细胞癌福尔马林固定石蜡包埋组织中lncRNA的定量分析。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2023-10-01 Epub Date: 2023-08-17 DOI: 10.2144/btn-2023-0033
Kiran Kumar, Kaveri Hallikeri, Ajaykumar Oli, Mallikarjun Goni, Apoorva Jain, Jagadeesha Poyya, Alagilavada S Shilpasree, Palaksha Kanive Javaregowda
{"title":"Quantitative analysis of lncRNA in formalin-fixed paraffin-embedded tissues of oral squamous cell carcinoma.","authors":"Kiran Kumar,&nbsp;Kaveri Hallikeri,&nbsp;Ajaykumar Oli,&nbsp;Mallikarjun Goni,&nbsp;Apoorva Jain,&nbsp;Jagadeesha Poyya,&nbsp;Alagilavada S Shilpasree,&nbsp;Palaksha Kanive Javaregowda","doi":"10.2144/btn-2023-0033","DOIUrl":"10.2144/btn-2023-0033","url":null,"abstract":"<p><p>The study evaluated expression profiles of few regulatory lncRNAs in oral squamous cell carcinoma and normal mucosa adjacent to oral cancer using paired fresh frozen and formalin-fixed paraffin-embedded (FFPE) tissues stored at a different duration of time (1-5 years) using real-time quantitative PCR. The quantity and quality of total RNA isolated from FFPE tissues was less compared with that of fresh frozen tissues, which resulted in a noncorrelation of quantification cycle values. Following normalization, the expression of lncRNAs in the paired tissues did not differ significantly. The differential expression of the lncRNAs in the study was consistent with The Cancer Genome Atlas head and neck squamous cell carcinoma database. The study findings demonstrate the possibility of performing accurate quantitative analysis of lncRNAs using short amplicons and standardized real-time quantitative PCR assays in oral squamous cell carcinoma FFPE samples.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"133-142"},"PeriodicalIF":2.7,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10005505","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
Peter and the Beanstalk: tackling the giant questions of soybean nodulation. 彼得和豆茎：解决大豆结瘤的巨大问题。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2023-09-01 Epub Date: 2023-08-17 DOI: 10.2144/btn-2023-0060
Peter Gresshoff
{"title":"Peter and the Beanstalk: tackling the giant questions of soybean nodulation.","authors":"Peter Gresshoff","doi":"10.2144/btn-2023-0060","DOIUrl":"10.2144/btn-2023-0060","url":null,"abstract":"<p><p>The following is an edited interview, carried out by the Journal Development Editor of <i>BioTechniques</i>, Ashling Cannon, with Peter Gresshoff (University of Queensland, UQ; Brisbane, Australia). Peter is a plant developmental geneticist, using molecular and genetic tools to understand the complexities of gene networks during the control of nodule formation in legumes. He was the Director of the Center of Excellence for Integrative Legume Research and is now an Emeritus Professor at UQ.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"75 3","pages":"95-98"},"PeriodicalIF":2.7,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10667503","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: 1
Education in microscopy: taking a closer look with Jennifer Waters. 显微镜教育：与詹妮弗·沃特斯一起仔细观察。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2023-09-01 Epub Date: 2023-08-29 DOI: 10.2144/btn-2023-0079
Jennifer Waters
{"title":"Education in microscopy: taking a closer look with Jennifer Waters.","authors":"Jennifer Waters","doi":"10.2144/btn-2023-0079","DOIUrl":"10.2144/btn-2023-0079","url":null,"abstract":"<p><p>Jennifer Waters (Nikon Imaging Center, Harvard Medical School, MA, USA) spoke to Ebony Torrington (Future Science Group, London, UK) about her career in microscopy and the importance of education. Jennifer is the Director of the Nikon Imaging Center (NIC) at Harvard Medical School and a Chan Zuckerberg Initiative (CZI) Imaging Scientist. She was trained in cell biology and microscopy by Ted Salmon at University of North Carolina (UNC) at Chapel Hill (NC, USA), where her research focused on mitosis and cell cycle regulation. Jennifer's main focus today, in addition to running the NIC, is developing light microscopy educational resources.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"75 3","pages":"91-94"},"PeriodicalIF":2.7,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10304060","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
Special Focus Issue - Celebrating 40 years of publishing lab techniques: looking back to look foreword. 焦点特刊-庆祝实验室技术出版40周年：回顾前言。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2023-09-01 DOI: 10.2144/btn-2023-0081
Beatrice Bowlby, Tristan Free, Annie Coulson, Aisha Al-Janabi, Ashling Cannon, Ebony Torrington
{"title":"Special Focus Issue - Celebrating 40 years of publishing lab techniques: looking back to look foreword.","authors":"Beatrice Bowlby, Tristan Free, Annie Coulson, Aisha Al-Janabi, Ashling Cannon, Ebony Torrington","doi":"10.2144/btn-2023-0081","DOIUrl":"10.2144/btn-2023-0081","url":null,"abstract":"","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"75 3","pages":"75-77"},"PeriodicalIF":2.7,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10303020","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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