BioTechniques最新文献_第2页

UK Biobank: what can it do, how you can use it and how is it being used?

IF 2.2 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

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":"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-ΔCt (or ΔCt) and 2-ΔΔCt 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 Drosophila melanogaster and Apis mellifera workers. The presented results reveal that our working strategy is reliable and highlight the efficacy and performance of qDATA application.","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

引用次数: 0

Characterization of nuclear microsatellites in Marchantia polymorpha (liverwort) with additional trans-specific analyses. 多态地茅（Marchantia polymorpha, liverwort）核微卫星的特征与额外的跨特异性分析。

IF 2.2 4区工程技术

BioTechniques Pub Date : 2024-11-01 Epub Date: 2024-12-25 DOI: 10.1080/07366205.2024.2445454

Nicole Rodriguez Ortiz, Niharika Sharma, Tian-Xiong Zheng, James J Campanella

引用次数: 0

Development of a human tyrosinase activity inhibition assay using human melanoma cell lysate. 利用人黑色素瘤细胞裂解液建立人酪氨酸酶活性抑制试验。

IF 2.2 4区工程技术

BioTechniques Pub Date : 2024-11-01 Epub Date: 2024-12-16 DOI: 10.1080/07366205.2024.2441637

Gengxuan Shi, Yunjiang Feng, Kathryn F Tonissen

引用次数: 0

Who wants to live forever? Models shaping the future of aging research. 谁想长生不老？塑造老龄化研究未来的模型。

IF 2.2 4区工程技术

BioTechniques Pub Date : 2024-11-01 Epub Date: 2025-01-06 DOI: 10.1080/07366205.2024.2445467

Annie Coulson

引用次数: 0

Optimized for routine: highly sensitive fluorescent Telomeric Repeat Amplification Protocol (f-TRAP). 常规优化：高灵敏度荧光端粒重复扩增协议（f-TRAP）。

IF 2.2 4区工程技术

BioTechniques Pub Date : 2024-10-01 Epub Date: 2024-12-15 DOI: 10.1080/07366205.2024.2432805

Silke Fähnrich, Anne Wedemann, Laura Steenpass, Wilhelm Gerhard Dirks

{"title":"Optimized for routine: highly sensitive fluorescent Telomeric Repeat Amplification Protocol (f-TRAP).","authors":"Silke Fähnrich, Anne Wedemann, Laura Steenpass, Wilhelm Gerhard Dirks","doi":"10.1080/07366205.2024.2432805","DOIUrl":"10.1080/07366205.2024.2432805","url":null,"abstract":"The strict suppression of telomerase activity (TA) in terminally differentiated human cells causes a shortening of the chromosome ends after each cell division. This tumor suppression surveillance mechanism is associated with a limited number of cell divisions known as Hayflick limit. Here we present an optimized protocol for measuring TA that combines a fluorescently labeled bait primer and polymerase chain reaction (PCR) amplification with analytical capillary electrophoresis (CE) to achieve a detection limit of one telomerase-positive cell per ten thousand negative cells. In research laboratories today, a broad panel of TRAP assay protocols enables the assessment of the immortality of newly generated cell lines or the unambiguous evaluation of the reprogramming of induced pluripotent stem cells (iPSCs). The present f-TRAP protocol, optimized for routine use, enables fast ad hoc application for single measurements up to a high throughput of mass samples using a triplicate approach of different lysate concentrations. Final CE analysis facilitates standardized data processing and storage for documentation of results and could make f-TRAP a useful assay in research and clinical oncology.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"517-522"},"PeriodicalIF":2.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142827093","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

Importance of a reference ladder in analytical testing of CRISPR HDR donor ssDNA templates. 参考阶梯在CRISPR HDR供体ssDNA模板分析测试中的重要性。

IF 2.2 4区工程技术

BioTechniques Pub Date : 2024-10-01 Epub Date: 2024-12-04 DOI: 10.1080/07366205.2024.2429308

Zhi-Xiang Lu, Anis H Khimani, Yanhong Tong

引用次数: 0

A single-cell 3D dynamic volume control system for chondrocytes. 软骨细胞单细胞三维动态体积控制系统

IF 2.2 4区工程技术

BioTechniques Pub Date : 2024-10-01 Epub Date: 2024-10-15 DOI: 10.1080/07366205.2024.2412414

Qiang Zhang, Yiyao Wang, Yanjun Zhang, Xiaochun Wei, Weiyi Chen, Quanyou Zhang

{"title":"A single-cell 3D dynamic volume control system for chondrocytes.","authors":"Qiang Zhang, Yiyao Wang, Yanjun Zhang, Xiaochun Wei, Weiyi Chen, Quanyou Zhang","doi":"10.1080/07366205.2024.2412414","DOIUrl":"10.1080/07366205.2024.2412414","url":null,"abstract":"In articular cartilage, zone-specific cellular morphology is a typical characteristic of cartilage tissue, which is related with chondrocyte function, inflammation and osteoarthritis (OA). Chondrocyte hypertrophic phenotype is a criticle physiological process which indicates a hallmark of chondrocyte terminal differentiation and bone formation. Thus, developing a in vitro cell culture system for dynamic regulation of single chondrocyte volume at a three-dimensional (3D) level is particularly necessary for understanding how physical cues of matrix microenvironment regulate chondrocyte fate and the degeneration of articular cartilage. Here, based on the soft lithography techniques, we have constructed well-defined single-cell 3D dynamic volume control system to recapitulate the physiological matrix microenvironment of single chondrocyte niche. The results of finite element analysis indicated that the stress and strain distribution in the cell culture region is homogeneous during the stretching process. Additionally, 3D dynamic volume expansion and compression of single cells in physiological or hyperphysiological can be realized in this cell culture system. Our device for single-cell 3D dynamic culture provides a microphysiological culture system for chondrocytes to explore the mechanisms of cartilage hypertrophy, as well as develops a new paradigm for functional cartilage tissue engineering and regenerative medicine.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"495-504"},"PeriodicalIF":2.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142457178","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 validation of a portable device for lab-free versatile nucleic acid extraction. 一种便携式无实验室多功能核酸提取装置的开发和验证。

IF 2.2 4区工程技术

BioTechniques Pub Date : 2024-10-01 Epub Date: 2024-12-02 DOI: 10.1080/07366205.2024.2427544

Anthony J Politza, Tianyi Liu, Aneesh Kshirsagar, Ming Dong, Md Ahasan Ahamed, Weihua Guan

{"title":"Development and validation of a portable device for lab-free versatile nucleic acid extraction.","authors":"Anthony J Politza, Tianyi Liu, Aneesh Kshirsagar, Ming Dong, Md Ahasan Ahamed, Weihua Guan","doi":"10.1080/07366205.2024.2427544","DOIUrl":"10.1080/07366205.2024.2427544","url":null,"abstract":"Nucleic acid testing (NAT) has revolutionized diagnostics by providing precise, rapid, and scalable detection methods for diverse biological samples. These recent advancements satisfy the increasing demand for on-site diagnostics, yet sample preparation remains a significant bottleneck for achieving highly sensitive diagnostic assays. There is an unmet need for compatible, efficient, and lab-free sample preparation for point-of-care NAT. To address this, we developed a portable, lab-free, and battery-powered device for extracting nucleic acids. We explored using low centrifugal forces with existing commercial chemistry, demonstrating excellent performance. We designed and tested a battery-powered device to enable lab-free extractions, and verified reagents stored out to 6 months, suggesting exceptional deployment capabilities. We evaluated our device, comparing our results against those from a benchtop centrifuge across three types of samples: HIV RNA in buffer, HIV RNA in plasma, and SARS-CoV-2 RNA in saliva. The portable device demonstrated excellent agreement with the benchtop centrifuge, indicating high reliability. By providing an effective on-site sample preparation solution, the widespread adoption of low centrifugal extractions will improve the sensitivity and reliability of NAT and will positively impact other point-of-care technologies such as next generation sequencing (NGS), biomarker detection, and environmental monitoring.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"505-515"},"PeriodicalIF":2.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765762","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