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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 : 2025-04-03 DOI: 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":"https://doi.org/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":"1-12"},"PeriodicalIF":2.2,"publicationDate":"2025-04-03","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}
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 : 2025-03-26 DOI: 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":"https://doi.org/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":"1-9"},"PeriodicalIF":2.2,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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":"<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":"","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":"","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
{"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}
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":"<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}
引用次数: 0
Opportunities and challenges in implementing CRISPR-based point-of-care testing for Monkeypox detection. 实施基于crispr的猴痘即时检测的机遇和挑战。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2025-02-01 Epub Date: 2025-04-03 DOI: 10.1080/07366205.2025.2473827
Md Ahasan Ahamed, Weihua Guan
{"title":"Opportunities and challenges in implementing CRISPR-based point-of-care testing for Monkeypox detection.","authors":"Md Ahasan Ahamed, Weihua Guan","doi":"10.1080/07366205.2025.2473827","DOIUrl":"10.1080/07366205.2025.2473827","url":null,"abstract":"","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"41-45"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771302","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 of an enhanced anti-pan-N-formylmethionine-specific antibody. 一种增强抗泛n-甲酰基蛋氨酸特异性抗体的研制。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2025-02-01 Epub Date: 2025-02-20 DOI: 10.1080/07366205.2025.2467583
Dasom Kim, Kyu-Sang Park, Cheol-Sang Hwang
{"title":"Development of an enhanced anti-pan-N-formylmethionine-specific antibody.","authors":"Dasom Kim, Kyu-Sang Park, Cheol-Sang Hwang","doi":"10.1080/07366205.2025.2467583","DOIUrl":"10.1080/07366205.2025.2467583","url":null,"abstract":"<p><p>Both bacterial and eukaryotic ribosomes can initiate protein synthesis with formylmethionine (fMet), but detecting fMet-bearing peptides and fMet-bearing proteins has been challenging due to the lack of effective anti-pan-fMet antibodies. Previously, we developed a polyclonal anti-fMet antibody using a fMet-Gly-Ser-Gly-Cys pentapeptide that detects those fMet-bearing peptides and fMet-bearing proteins regardless of their sequence context. In this study, we significantly improved the antibody's specificity and affinity by using a mixture of fMet-Xaa-Cys tripeptides (Xaa, any of the 20 amino acids) as the immunogen. This newly optimized anti-fMet antibody is a powerful, cost-effective tool for detecting fMet-bearing proteins across species. Furthermore, this approach provides a foundation for developing anti-pan-specific antibodies targeting other N-terminal modifications through acylation, alkylation, oxidation, arginylation, etc.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"46-55"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456607","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
Correction. 修正。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2025-01-16 DOI: 10.1080/07366205.2025.2450187
{"title":"Correction.","authors":"","doi":"10.1080/07366205.2025.2450187","DOIUrl":"https://doi.org/10.1080/07366205.2025.2450187","url":null,"abstract":"","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"1-2"},"PeriodicalIF":2.2,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142999302","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
Uncovering the molecular mechanisms behind Alzheimer's and Parkinson's disease through multi-omics: an interview with Bruno A. Benitez. 通过多组学揭示阿尔茨海默病和帕金森病背后的分子机制：采访布鲁诺·a·贝尼特斯。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2025-01-01 Epub Date: 2025-01-31 DOI: 10.1080/07366205.2025.2457900
Bruno A Benitez
{"title":"Uncovering the molecular mechanisms behind Alzheimer's and Parkinson's disease through multi-omics: an interview with Bruno A. Benitez.","authors":"Bruno A Benitez","doi":"10.1080/07366205.2025.2457900","DOIUrl":"10.1080/07366205.2025.2457900","url":null,"abstract":"","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"5-8"},"PeriodicalIF":2.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063427","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
Analytical validation of the IBD segment-based tool KinSNP® for human identification applications. 基于IBD片段的工具KinSNP®用于人类鉴定应用的分析验证。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2025-01-01 Epub Date: 2025-01-18 DOI: 10.1080/07366205.2025.2454770
Bruce Budowle, Jianye Ge, Lee Baker, Kristen Mittelman, David Mittelman
{"title":"Analytical validation of the IBD segment-based tool KinSNP<sup>®</sup> for human identification applications.","authors":"Bruce Budowle, Jianye Ge, Lee Baker, Kristen Mittelman, David Mittelman","doi":"10.1080/07366205.2025.2454770","DOIUrl":"10.1080/07366205.2025.2454770","url":null,"abstract":"<p><p>KinSNP<sup>®</sup> v1.0, a software tool for human identification, has been widely used to measure IBD segment sharing between individuals using dense SNP data. Herein, the tool was validated using simulated pedigree data (up to 9<sup>th</sup> degree relationships) from five diverse populations from the 1000 Genomes Project. Performance was further tested under conditions of simulated genotyping errors and allele or locus dropout. KinSNP data were benchmarked with IBIS, Ped-sim, and known ranges of centimorgan sharing. The calculated values from KinSNP aligned closely with IBIS and Ped-sim benchmarks, and accuracy was maintained with up to 75% simulated missing data. However, even slight increases in simulated sequence error rates negatively impacted performance. This study supports that KinSNP is a reliable solution for IBD-based analyses in forensic contexts.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"9-22"},"PeriodicalIF":2.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142999164","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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