BioTechniques最新文献_第5页

A clinical biomarker assay to quantitate CXCL9 in human serum. 定量测定人血清中CXCL9的临床生物标志物试验。

IF 2.6 4区工程技术

BioTechniques Pub Date : 2025-11-01 Epub Date: 2026-01-29 DOI: 10.1080/07366205.2026.2618960

Lucia Franco-Dilone, Oitak Allen Wong, Omar F Laterza, Xuemei Zhao

引用次数: 0

Pre-sequencing assessment of RNA-Seq library quality using real-time qPCR. 利用实时qPCR对RNA-Seq文库质量进行测序前评估。

IF 2.5 4区工程技术

BioTechniques Pub Date : 2025-09-01 Epub Date: 2025-11-26 DOI: 10.1080/07366205.2025.2590943

Kavya Kottapalli, Hsu Chao, Qi Jiang, Jimmonique Donelson, Nathanael Emerick, Sravya V Bhamidipati, Zeineen Momin, Tittu Mathew, Ziad M Khan, Viktoriya Korchina, Marie-Claude Gingras, Donna Muzny, Richard Gibbs, Harsha Doddapaneni

{"title":"Pre-sequencing assessment of RNA-Seq library quality using real-time qPCR.","authors":"Kavya Kottapalli, Hsu Chao, Qi Jiang, Jimmonique Donelson, Nathanael Emerick, Sravya V Bhamidipati, Zeineen Momin, Tittu Mathew, Ziad M Khan, Viktoriya Korchina, Marie-Claude Gingras, Donna Muzny, Richard Gibbs, Harsha Doddapaneni","doi":"10.1080/07366205.2025.2590943","DOIUrl":"10.1080/07366205.2025.2590943","url":null,"abstract":"RNA sequencing (RNA-Seq) is an essential assay for studying transcriptome profiling. Ribosomal RNA (rRNA) comprises more than 80-90% of total cellular RNA; efficient removal is essential for accurately capturing transcriptomes, particularly to sequence low-abundance mRNAs. Inefficient rRNA removal during library preparation can result from variations in sample quality, preparation methods, and handling. Estimating rRNA content in RNA-Seq libraries pre-sequencing is therefore challenging due to the absence of a reliable and cost-effective assessment method. This study addresses the issue by introducing a scalable real-time quantitative polymerase chain reaction (qPCR) based assay targeting human 18S rRNA to evaluate rRNA depletion efficiency of RNA-Seq libraries pre-sequencing. qPCR efficiency was optimized using serial dilutions of Universal Human Reference (UHR) control, and Ct thresholds were established using pilot data from 644 libraries. Following this optimization, analysis of 1748 human Total RNA-Seq libraries and 445 Poly A + two widely used RNA-Seq library methods, demonstrated a strong correlation between 18S rRNA qPCR results and post-sequencing rRNA rates. This assay was also used to evaluate the performance of Oligo (dT) beads from four different vendors to enrich mRNA. This 18S rRNA qPCR assay is a cost-effective, scalable approach for reliably predicting rRNA read percentage in RNA-Seq libraries pre-sequencing.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"319-329"},"PeriodicalIF":2.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145602102","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

Standardizing caloric restriction for preclinical cancer research. 规范临床前癌症研究的热量限制。

IF 2.6 4区工程技术

BioTechniques Pub Date : 2025-09-01 Epub Date: 2025-10-24 DOI: 10.1080/07366205.2025.2577029

Jenna L Jacoby, Ali Calderon Aparicio, Noëlle B François, Mehek Thapar, Sara E Burke, Shan Xu, Tiziana DeAngelis, Anuradha Shastri, Phuoc T Tran, Nicole L Simone

{"title":"Standardizing caloric restriction for preclinical cancer research.","authors":"Jenna L Jacoby, Ali Calderon Aparicio, Noëlle B François, Mehek Thapar, Sara E Burke, Shan Xu, Tiziana DeAngelis, Anuradha Shastri, Phuoc T Tran, Nicole L Simone","doi":"10.1080/07366205.2025.2577029","DOIUrl":"10.1080/07366205.2025.2577029","url":null,"abstract":"Despite increasing rates of metabolic syndrome, cancer treatment regimens often ignore the underlying metabolic dysfunction in patients. A high proportion of cancer patients have metabolic dysfunction, and caloric restriction has shown the potential to improve cancer treatment response. However, preclinical efficacy is hindered by inconsistent protocols. We demonstrated that a CR (caloric restriction) diet enhances radiotherapy outcome by promoting apoptosis and downregulating cell survival pathways in mice. However, CR animal models implementation greatly differs in previous cancer studies, hindering its clinical translation. Here, we propose an effective CR protocol that safely achieves a 30% caloric reduction in two weeks. Week one involves single housing the mice and taking individual caloric intake measurements across four days. Week two involves weaning the mice to a 30% reduction by reducing their caloric intake by 10% every other day, which allows for a safe reduction. This protocol integrates individualized intake measurement, gradual weaning, and real-time monitoring-features rarely combined in prior models-offering a reproducible and translationally relevant framework for cancer studies.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"345-354"},"PeriodicalIF":2.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13274516/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145353652","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

Taking root: the techniques growing genetically engineered plants. 生根发芽：种植转基因植物的技术。

IF 2.5 4区工程技术

BioTechniques Pub Date : 2025-09-01 Epub Date: 2025-09-17 DOI: 10.1080/07366205.2025.2560832

Beatrice Bowlby

引用次数: 0

Streamlining single-cell spatial transcriptomics for human kidney tissue. 简化人类肾脏组织单细胞空间转录组学。

IF 2.5 4区工程技术

BioTechniques Pub Date : 2025-09-01 Epub Date: 2025-12-01 DOI: 10.1080/07366205.2025.2591484

Son Vo, Kieran Meadows, Han Do, Kevin Chapman, Graciela Andonegui, Daniel A Muruve, Thang Pham, Justin Chun

{"title":"Streamlining single-cell spatial transcriptomics for human kidney tissue.","authors":"Son Vo, Kieran Meadows, Han Do, Kevin Chapman, Graciela Andonegui, Daniel A Muruve, Thang Pham, Justin Chun","doi":"10.1080/07366205.2025.2591484","DOIUrl":"10.1080/07366205.2025.2591484","url":null,"abstract":"Single-cell spatial technologies have emerged in recent years, enabling characterization of tissue architecture and organization at unprecedented resolution. However, computational analysis of spatial transcriptomics data remains a bottleneck for scientific discoveries in the absence of dedicated bioinformatics expertise. Here, we describe a novel cell area normalization method and workflow to annotate 15 kidney cell types from a dataset generated using NanoString's CosMx single-cell-resolution spatial transcriptomic platform. This approach enabled a comparison between two healthy kidney biopsies and two diseased samples. We validated our pipeline's accuracy using gene expression analysis, demonstrating increased sensitivity compared with other normalization methods and consistency with pathological changes observed in biopsy-proven diabetic kidney disease (DKD). Using precise cell type annotation, we observed significant changes in the proportions of podocytes and immune cells in DKD, with regional enrichment of immune cells and differential gene expression. Injured proximal tubules showed the expected upregulation of HAVCR1 and VCAM1, as well as other genes associated with diabetes, including IL18, ITGA3, and ITGB1. The workflow, now fully integrated into the BioTuring SpatialX (Lens V2.0), is available as a platform designed for users with no formal bioinformatics training, providing accessible web-based tools for spatial data analysis.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"331-344"},"PeriodicalIF":2.5,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145647241","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

Nondestructive DNA extraction from specimens and bulk samples preserved in DESS solution for DNA barcoding. 从保存在DESS溶液中的标本和大样本中进行无损DNA提取，用于DNA条形码。

IF 2.5 4区工程技术

BioTechniques Pub Date : 2025-07-01 Epub Date: 2025-08-07 DOI: 10.1080/07366205.2025.2542023

Eri Ogiso-Tanaka, Minako Abe Ito, Daisuke Shimada

引用次数: 0

An E. coli two-hybrid system to investigate human protein-protein interactions. 大肠杆菌双杂交系统研究人类蛋白质-蛋白质相互作用。

IF 2.6 4区工程技术

BioTechniques Pub Date : 2025-07-01 Epub Date: 2025-08-20 DOI: 10.1080/07366205.2025.2542028

Rebecca M Richardson, Sarah M Ho, Lane Tong, Morgan G Daniels, Steven M Pascal

{"title":"An E. coli two-hybrid system to investigate human protein-protein interactions.","authors":"Rebecca M Richardson, Sarah M Ho, Lane Tong, Morgan G Daniels, Steven M Pascal","doi":"10.1080/07366205.2025.2542028","DOIUrl":"10.1080/07366205.2025.2542028","url":null,"abstract":"The LexA-E. coli two-hybrid (LexA-E2H) system was initially developed to study interactions between microbial proteins in an Escherichia coli (E. coli) environment. We here demonstrate its utility for studying mammalian protein interactions. Specifically, this study uses LexA-E2H to provide the first direct and quantitative validation of Glucose Regulated Protein 78 (GRP78) binding to the cleaved-Prostate Apoptosis Response 4 (cl-Par-4) tumor suppressor. Furthermore, the results establish that this interaction does not require phosphorylation of either protein. MacConkey agar was used for initial detection of the interaction through colorimetric colony screening, distinguishing pale white-pink colonies (+ interaction) from red colonies (- interaction). This was followed by β-galactosidase assays for quantitative assessment. These results demonstrate the potential of the LexA-E2H system to advance human protein-protein interaction research. LexA-E2H is simple to implement, avoiding the need to culture eukaryotic cells, and bypassing interference from eukaryotic proteins. This system is ideal for laboratories with limited resources and complements conventional eukaryotic methods.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"283-295"},"PeriodicalIF":2.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12430536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144881989","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

Impact of ambient temperature exposure on miRNA stability in human plasma. 环境温度暴露对人血浆中miRNA稳定性的影响。

IF 2.6 4区工程技术

BioTechniques Pub Date : 2025-07-01 Epub Date: 2025-09-08 DOI: 10.1080/07366205.2025.2555657

Véronique Desgagné, Flore Lavoie, Imad Soukar, Marie-France Hivert, Luigi Bouchard, Perrie F O'Tierney-Ginn

{"title":"Impact of ambient temperature exposure on miRNA stability in human plasma.","authors":"Véronique Desgagné, Flore Lavoie, Imad Soukar, Marie-France Hivert, Luigi Bouchard, Perrie F O'Tierney-Ginn","doi":"10.1080/07366205.2025.2555657","DOIUrl":"10.1080/07366205.2025.2555657","url":null,"abstract":"MicroRNAs (miRNAs) are considered more stable than mRNA, but the impact of progressive thawing of biological samples after freezing as may happen during shipping delays has not been quantified. To address this, we utilized digital PCR to estimate the absolute concentrations of select miRNAs following progressive thawing of human plasma and maintenance at ambient temperature. Specifically, we quantified let-7b-3p, miR-144-5p, miR-150-5p, miR-517a-3p, miR-524-5p, and miR-1283, which have varying abundance in plasma. We observed a trend indicating a decline in miRNA concentration as plasma samples were progressively thawed. Notably, miR-150-5p and miR-517a-3p were the least stable and were degraded by 32% and 52% respectively after 24 hours of ambient temperature storage. We found that the variation in sensitivity to temperature was not due to the GC content of the miRNAs nor their initial abundance, suggesting that other factors, such as protein interactors and vesicles carrying these miRNAs, may impact sensitivity.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"271-282"},"PeriodicalIF":2.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973276/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145013838","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

How do you measure the success and impact of a core facility? 你如何衡量一个核心设施的成功和影响？

IF 2.5 4区工程技术

BioTechniques Pub Date : 2025-07-01 Epub Date: 2025-09-11 DOI: 10.1080/07366205.2025.2555118

Kara A Clissold, Michelle S Itano

引用次数: 0

Optimizing chromosome yield: a comparative analysis of harvesting, preparation and waste recovery methods. 优化染色体产量：收获、制备和废物回收方法的比较分析。

IF 2.5 4区工程技术

BioTechniques Pub Date : 2025-05-01 Epub Date: 2025-08-11 DOI: 10.1080/07366205.2025.2536438

Sarah L Berger, Rinyaporn Phengchat, Stanley W Botchway, Mohammed Yusuf

{"title":"Optimizing chromosome yield: a comparative analysis of harvesting, preparation and waste recovery methods.","authors":"Sarah L Berger, Rinyaporn Phengchat, Stanley W Botchway, Mohammed Yusuf","doi":"10.1080/07366205.2025.2536438","DOIUrl":"10.1080/07366205.2025.2536438","url":null,"abstract":"In mitotic chromosome preparation, it is crucial to maximize chromosome yield for downstream cytogenetic analysis. Using HeLa cells as a model adherent cell, we assessed and compared the recovery of chromosomes from the entire process as well as the fraction of chromosomes that would generally become discarded in the standardly used trypsinization and mitotic-shake-off chromosome preparation methods. A higher chromosome yield for polyamine (PA) and methanol acetic acid (MAA) chromosomes was achieved using the mitotic-shake-off method compared to trypsinization. Moreover, mitotic arrest using colcemid or nocodazole gave similar PA and MAA chromosome yields in the commonly collected fractions. Interestingly, when comparing the fractions that would usually be discarded in the mitotic-shake-off, for colcemid-treated cells compared to nocodazole-treated cells, a greater number of PA chromosomes was recovered from the former. Our results show that chromosomes can be retrieved from the waste media. These recovered chromosomes display a suitable morphology in all chromosome preparations, suggesting that in conditions where high chromosome yields are required, utilizing the mitotic-shake-off method and recovering the generally discarded chromosome fraction together with the commonly used fraction would aid in maximizing chromosome yield.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"245-256"},"PeriodicalIF":2.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820482","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