BioTechniquesPub Date : 2025-05-19DOI: 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
{"title":"Integration of mass cytometry and single-cell RNA-sequencing of cells in bronchoalveolar lavage.","authors":"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","doi":"10.1080/07366205.2025.2505347","DOIUrl":"https://doi.org/10.1080/07366205.2025.2505347","url":null,"abstract":"<p><p>Single-cell RNA sequencing (sc-RNA-seq) is a popular method for characterization of cell populations. However, the relationship between RNA and protein expression in cells is often discordant. Protein-based detection methods, such as cytometry by time-of-flight (CyTOF), can provide complementary data to sc-RNA-seq. We collected bronchoalveolar lavage (BAL) from healthy participants and co-evaluated cell populations and gene/protein expression by applying sc-RNA-seq and CyTOF to the same samples. Cell populations were well correlated between these two platforms, but differences emerged at the sub-population level. Notably, macrophage subtypes did not correlate well; whereas T-lymphocytes did. Gene and protein expression levels were significantly correlated (<i>p</i> < .01). Overall, we recommend CyTOF as a tool to validate sc-RNA-seq data for select proteins and cell populations in BAL samples.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"1-12"},"PeriodicalIF":2.2,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092566","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}
BioTechniquesPub Date : 2025-03-01Epub Date: 2025-05-23DOI: 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
{"title":"Freezing diluted bovine serum albumin standards does not significantly affect standard curves.","authors":"Rachelle Sheets, Bhavik Rajaboina, Caitlin E Bromberg, Liam P Curtin, Mitchell L Haddock, Phillip Stafford, Theresa Currier Thomas, Adrienne C Scheck","doi":"10.1080/07366205.2025.2502268","DOIUrl":"10.1080/07366205.2025.2502268","url":null,"abstract":"<p><p>Total protein isolation followed by quantitation using a colorimetric method, such as the bicinchoninic acid (BCA) assay is a common laboratory protocol. Protein concentrations are determined by comparing extracted samples to a standard curve generated from serial dilutions of a reference protein, such as bovine serum albumin (BSA). This study aimed to identify the most reproducible and accurate method for quantifying protein concentrations in an experimental series over time. We analyzed the effect of serial freeze-thaws, inter-person and intra-person variability in standard preparation and assay execution. Absorbance was measured at 565 nanometers (nm) using an Epoch Microplate Spectrophotometer (Agilent Technologies, Inc., Santa Clara, CA) with Gen5 Data Analysis software. The most consistent and accurate method for determining the protein concentrations over time is to prepare a large batch of diluted BSA standards, aliquot them into small portions, and store them frozen.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"77 3","pages":"95-102"},"PeriodicalIF":2.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126559","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}
BioTechniquesPub Date : 2025-03-01Epub Date: 2025-05-23DOI: 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":"<p><p>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.</p>","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}
BioTechniquesPub Date : 2025-03-01Epub Date: 2025-03-26DOI: 10.1080/07366205.2025.2483601
Charles Polen, Esmeralda Mendez Ortiz, Cordelia Harbison, Nate Garringer, Martin Lopez, Kristy L Kounovsky-Shafer
{"title":"Developing an insert to protect large DNA molecules during cell lysis.","authors":"Charles Polen, Esmeralda Mendez Ortiz, Cordelia Harbison, Nate Garringer, Martin Lopez, Kristy L Kounovsky-Shafer","doi":"10.1080/07366205.2025.2483601","DOIUrl":"10.1080/07366205.2025.2483601","url":null,"abstract":"<p><p>Determining large structural variations is difficult and time-consuming without long molecules to aid in the genome assembly. One issue is the fragility of large DNA molecules during routine molecular biology techniques. A novel inverted agarose insert was created to protect and make accessing large DNA easier. The inverted agarose insert has the cell solution in the middle and the agarose on the outside rather than the cells embedded in the agarose (plug inserts). Multiple agarose concentrations were tested to determine the best percentage of agarose to create the inverted insert. A proof-of-principle inverted insert was tested with <i>S. cerevisiae</i> cells to show that cells could be lysed inside the inverted insert, allowing the DNA to remain at full length in the middle.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"103-111"},"PeriodicalIF":2.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12101932/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143708317","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}
{"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":"<p><strong>Background: </strong>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.</p><p><strong>Objective: </strong>SphereRing<sup>®</sup> 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.</p><p><strong>Method: </strong>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.</p><p><strong>Results: </strong>ChatGPT Data Analyst was consistent with ImageJ for all parameters. Bland-Altman plots demonstrated strong agreement; most data points were within the 95% limits.</p><p><strong>Conclusion: </strong>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.</p>","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}
BioTechniquesPub Date : 2025-03-01Epub Date: 2025-04-03DOI: 10.1080/07366205.2025.2484094
Farida Emran, Ibrahim Kays, Chiu-An Lo, Yueyang Li, Brian E Chen
{"title":"A drug screening platform for protein expression levels in neurological disorders.","authors":"Farida Emran, Ibrahim Kays, Chiu-An Lo, Yueyang Li, Brian E Chen","doi":"10.1080/07366205.2025.2484094","DOIUrl":"10.1080/07366205.2025.2484094","url":null,"abstract":"<p><p>Neurological and psychiatric diseases and disorders affect more than half of the population. Many of these diseases are caused by the malfunctioning of protein synthesis, where too little or too much production of a protein harms a cell and its functions within the brain. We developed a drug screening platform to identify compounds that target the primary cause of these diseases, namely protein expression amounts. This cellular assay monitors protein expression of a target disease gene along with the protein expression of a control gene using the Protein Quantitation Ratioing (PQR) technique. PQR tracks protein concentration using fluorescence. We used human cells and CRISPR-Cas9 genome editing to insert the <i>Protein Quantitation Reporter</i> into target genes. These cells are used in high-throughput drug screening measuring the fluorescence as the assay. Drug hits can be validated using the same PQR technique or animal models of the disease.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"113-124"},"PeriodicalIF":2.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771300","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}
BioTechniquesPub Date : 2025-02-01Epub Date: 2025-03-12DOI: 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":"<p><p>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.</p>","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}
BioTechniquesPub Date : 2025-02-01Epub Date: 2025-02-20DOI: 10.1080/07366205.2025.2467584
Ryuhei Kinami, Toshinao Ineno
{"title":"Alkaline dip DNA extraction from skin mucus for high-throughput sexing of sterlets (<i>Acipenser ruthenus</i>).","authors":"Ryuhei Kinami, Toshinao Ineno","doi":"10.1080/07366205.2025.2467584","DOIUrl":"10.1080/07366205.2025.2467584","url":null,"abstract":"<p><p>Studies on simple DNA extraction methods from fish mucus, which is an ideal resource for noninvasive sampling, are scarce. In the aquaculture of sturgeons such as sterlets (<i>Acipenser ruthenus</i>), a high-throughput genetic sexing method is needed, as only females are reared to maturity for their roe. Here, DNA extraction methods using HotSHOT (hot sodium hydroxide and tris), a novel alkaline dip, alkaline glycol, and water were compared using the skin mucus of sterlets (n = 8) collected with a toothpick. High-throughput sexing of sterlets from six production batches (n = 3953) was also evaluated using HotSHOT or alkaline dip. An alkaline dip with 10-25 mM NaOH was an effective alternative to HotSHOT, eliminating the heating and neutralizing steps. Regarding high-throughput sexing, > 99% (3946) individuals were successfully genotyped on the first PCR trial, and genotype ratios of each batch were close to 1:1, showing applicability of the alkaline dip method for practical sterlet sexing.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"56-65"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466823","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}
BioTechniquesPub Date : 2025-02-01Epub Date: 2025-02-26DOI: 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":"<p><p>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.</p>","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}