BioTechniques最新文献

Integration of mass cytometry and single-cell RNA-sequencing of cells in bronchoalveolar lavage. 支气管肺泡灌洗细胞的细胞细胞计数和单细胞rna测序的整合。

IF 2.2 4区工程技术

BioTechniques Pub Date : 2025-05-19 DOI: 10.1080/07366205.2025.2505347

Elizabeth Guinto, Sameeksha Chopra, I-Chih Kuo, Samuel B Shin, Melina Messing, Chung Y Cheung, Julia Sw Yang, Firoozeh V Gerayeli, William Yip, Stephen Milne, Rachel L Eddy, Janice M Leung, Kelly M McNagny, Don D Sin

引用次数: 0

Correction. 修正。

IF 2.2 4区工程技术

BioTechniques Pub Date : 2025-03-01 Epub Date: 2025-01-16 DOI: 10.1080/07366205.2025.2450187

引用次数: 0

Freezing diluted bovine serum albumin standards does not significantly affect standard curves. 冷冻稀释牛血清白蛋白标准品对标准曲线影响不显著。

IF 2.2 4区工程技术

BioTechniques Pub Date : 2025-03-01 Epub Date: 2025-05-23 DOI: 10.1080/07366205.2025.2502268

Rachelle Sheets, Bhavik Rajaboina, Caitlin E Bromberg, Liam P Curtin, Mitchell L Haddock, Phillip Stafford, Theresa Currier Thomas, Adrienne C Scheck

引用次数: 0

Standardized droplet preamplification method for downstream circulating cell-free DNA analysis. 标准化滴滴预扩增法用于下游循环无细胞DNA分析。

IF 2.2 4区工程技术

BioTechniques Pub Date : 2025-03-01 Epub Date: 2025-05-23 DOI: 10.1080/07366205.2025.2504287

Colin Skeen, Erica D Pratt

{"title":"Standardized droplet preamplification method for downstream circulating cell-free DNA analysis.","authors":"Colin Skeen, Erica D Pratt","doi":"10.1080/07366205.2025.2504287","DOIUrl":"https://doi.org/10.1080/07366205.2025.2504287","url":null,"abstract":"Circulating cell-free DNA (ccfDNA) can be found in blood and other biofluids and is a minimally invasive biomarker for several pathological processes. As tumors become more invasive, an increasing amount of circulating tumor DNA (ctDNA) is also shed into the peripheral circulation. Combined analysis of ccfDNA and ctDNA has demonstrated prognostic and predictive value in metastatic disease. However, localized tumors shed significantly less ccfDNA/ctDNA and accurate detection remains a technical challenge. To overcome this barrier, droplet preamplification has been used to perform robust multiplexed analysis of low-input samples. To reduce false positives, it is essential to use a high-fidelity polymerase with 3'-5' exonuclease activity. However, attempts to combine high-fidelity polymerases with commercial droplet digital chemistries have had limited success. There is also no standardized method for efficient amplicon recovery from droplets. In this work, we present a method to reliably stabilize emulsions and recover preamplified templates. We systematically compared our protocol with different destabilization methods and found an average 41% improvement in recovery efficiency. We anticipate that this standardized method will increase the consistency and reproducibility of ccfDNA/ctDNA analyses. This technique could be readily translated to other low-input or low-biomass samples, such as urine, saliva, or archived biopsy specimens.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"77 3","pages":"125-135"},"PeriodicalIF":2.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126564","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 an insert to protect large DNA molecules during cell lysis. 开发一种插入物，在细胞裂解过程中保护大的DNA分子。

IF 2.2 4区工程技术

BioTechniques Pub Date : 2025-03-01 Epub Date: 2025-03-26 DOI: 10.1080/07366205.2025.2483601

Charles Polen, Esmeralda Mendez Ortiz, Cordelia Harbison, Nate Garringer, Martin Lopez, Kristy L Kounovsky-Shafer

引用次数: 0

Efficient spheroid morphology assessment with a ChatGPT data analyst: implications for cell therapy. 高效球体形态评估与ChatGPT数据分析：对细胞治疗的影响。

IF 2.2 4区工程技术

BioTechniques Pub Date : 2025-03-01 Epub Date: 2025-04-23 DOI: 10.1080/07366205.2025.2493489

Takuya Sakamoto, Hiroto Koma, Ayane Kuwano, Tetsuhiro Horie, Atsushi Fuku, Hironori Kitajima, Yuka Nakamura, Ikuhiro Tanida, Yujiro Nakade, Hiroaki Hirata, Yoshiyuki Tachi, Hiroshi Sunami, Daisuke Sakamoto, Sohsuke Yamada, Naoki Yamamoto, Yusuke Shimizu, Yasuhito Ishigaki, Toru Ichiseki, Ayumi Kaneuji, Satoshi Osawa, Norio Kawahara

{"title":"Efficient spheroid morphology assessment with a ChatGPT data analyst: implications for cell therapy.","authors":"Takuya Sakamoto, Hiroto Koma, Ayane Kuwano, Tetsuhiro Horie, Atsushi Fuku, Hironori Kitajima, Yuka Nakamura, Ikuhiro Tanida, Yujiro Nakade, Hiroaki Hirata, Yoshiyuki Tachi, Hiroshi Sunami, Daisuke Sakamoto, Sohsuke Yamada, Naoki Yamamoto, Yusuke Shimizu, Yasuhito Ishigaki, Toru Ichiseki, Ayumi Kaneuji, Satoshi Osawa, Norio Kawahara","doi":"10.1080/07366205.2025.2493489","DOIUrl":"10.1080/07366205.2025.2493489","url":null,"abstract":"Background: Adipose-derived stem cells (ADSCs) exhibit promising potential for the treatment of various diseases, including osteoarthritis. Spheroids derived from ADSCs are a viable treatment option with enhanced anti-inflammatory effects and tissue repair capabilities.Objective: SphereRing® is a rotating donut-shaped tube that efficiently produces large quantities of spheroids. However, accurately measuring spheroid size for spheroid quality assessment is challenging. This study aimed to develop an automated method for measuring spheroid size using deep learning through the ChatGPT Data Analyst for image recognition and processing.Method: The area, perimeter, and circularity of spheroids generated with the SphereRing system were analyzed using ChatGPT Data Analyst and ImageJ. Measurement accuracy was validated using Bland-Altman analysis and scatter plot correlation coefficients.Results: ChatGPT Data Analyst was consistent with ImageJ for all parameters. Bland-Altman plots demonstrated strong agreement; most data points were within the 95% limits.Conclusion: The ChatGPT Data Analyst provides a reliable and efficient alternative for assessing spheroid quality. This method reduces human error and improves reproducibility to enhance spheroid quality control. Thus, this method has potential applications in regenerative medicine.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"137-149"},"PeriodicalIF":2.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143958147","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 drug screening platform for protein expression levels in neurological disorders. 神经系统疾病蛋白表达水平的药物筛选平台。

IF 2.2 4区工程技术

BioTechniques Pub Date : 2025-03-01 Epub Date: 2025-04-03 DOI: 10.1080/07366205.2025.2484094

Farida Emran, Ibrahim Kays, Chiu-An Lo, Yueyang Li, Brian E Chen

引用次数: 0

Impact of commercial RNA extraction methods on the recovery of human RNA sequence data from archival fixed tissues. 商业RNA提取方法对从档案固定组织中恢复人类RNA序列数据的影响。

IF 2.2 4区工程技术

BioTechniques Pub Date : 2025-02-01 Epub Date: 2025-03-12 DOI: 10.1080/07366205.2025.2473842

Tess Wilson, Melanie Kuch, Debi Poinar, Jasmine Rockarts, Bruce Wainman, Susan Morgello, Hendrik Poinar

{"title":"Impact of commercial RNA extraction methods on the recovery of human RNA sequence data from archival fixed tissues.","authors":"Tess Wilson, Melanie Kuch, Debi Poinar, Jasmine Rockarts, Bruce Wainman, Susan Morgello, Hendrik Poinar","doi":"10.1080/07366205.2025.2473842","DOIUrl":"10.1080/07366205.2025.2473842","url":null,"abstract":"Archival fixed tissues hold key insights into the evolutionary history of RNA viruses and the associated host immune response, yet access to the RNA sequence data is limited by a lack of robust methods for RNA extraction and sequence retrieval from these tissue types. Here we compared three commercial RNA extraction techniques (bead, column, and phase-based) on five fixed human brain tissues done in triplicate, that have been stored for up to 43 years. We found that for this sample set, bead-based extractions captured longer molecules and yielded a greater proportion of unique reads when aligned to the human genome, than did column and phase-based extraction methods. Via the incorporation of multiple extraction replicates, we quantified the variability in sequencing metrics resulting from tissue sample and extraction technique heterogeneity. Additionally, we compared pre- and post-sequencing metrics and found that the former poorly predicted post-sequencing on-target success. Our findings help inform future research on the recovery of RNA from archival fixed tissues.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"76-93"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12063700/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603124","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

Alkaline dip DNA extraction from skin mucus for high-throughput sexing of sterlets (Acipenser ruthenus). 从皮肤黏液中提取碱液DNA用于小鲟高通量性别鉴定。

IF 2.2 4区工程技术

BioTechniques Pub Date : 2025-02-01 Epub Date: 2025-02-20 DOI: 10.1080/07366205.2025.2467584

Ryuhei Kinami, Toshinao Ineno

引用次数: 0

Utilizing the biosimulator to analyze the environmental microbiome within the intensive care units of a hospital. 利用生物模拟器分析医院重症监护病房内的环境微生物组。

IF 2.2 4区工程技术

BioTechniques Pub Date : 2025-02-01 Epub Date: 2025-02-26 DOI: 10.1080/07366205.2025.2467550

Sunil Thomas, Kyle Bittinger, Lawrence L Livornese

{"title":"Utilizing the biosimulator to analyze the environmental microbiome within the intensive care units of a hospital.","authors":"Sunil Thomas, Kyle Bittinger, Lawrence L Livornese","doi":"10.1080/07366205.2025.2467550","DOIUrl":"10.1080/07366205.2025.2467550","url":null,"abstract":"Hospital-acquired infections (HAIs), also known as nosocomial infections, are illnesses contracted during treatment at a healthcare facility and can result in severe or life-threatening complications. HAIs are caused by microorganisms that exhibit resistance to standard antibiotics. HAIs can lead to severe complications, longer stays, and increased mortality, particularly in vulnerable patients. In our previous study, we demonstrated the ability of an engraved Petri dish, referred to as a \"biosimulator,\" to induce adhesion of non-adherent cells and the microbiome. This paper explores the use of the biosimulator to elucidate the microbiome composition within intensive care units (ICUs) in a hospital setting. The biosimulator, with a nutrient-rich bacterial growth medium, was placed in ICUs for 24 h, then incubated for three days under aerobic and anaerobic conditions. Using 16S rRNA sequencing, we profiled the ICU microbiome from multiple samples. Our findings showed that ICU microbiomes closely mirrored those of patients, with microorganisms in the ICU exhibiting stronger interrelationships than in control conditions. The combined use of the biosimulator and profiling offers an effective approach for analyzing and understanding microbiome changes in healthcare settings, particularly in high-risk areas, such as ICUs.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"66-75"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514676","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