{"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":"https://doi.org/10.1080/07366205.2024.2412414","url":null,"abstract":"<p><p>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 <i>in vitro</i> 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.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-15","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}
BioTechniquesPub Date : 2024-09-13DOI: 10.1080/07366205.2024.2397284
James D Feller,Leah Colton
{"title":"Comparison of commercially available DNA and RNA extraction kits for wildlife feces collected from the environment.","authors":"James D Feller,Leah Colton","doi":"10.1080/07366205.2024.2397284","DOIUrl":"https://doi.org/10.1080/07366205.2024.2397284","url":null,"abstract":"Wildlife fecal samples were collected across two Air Force installations to evaluate the effectiveness of commercially available DNA and RNA extraction kits. Four DNA kits, two DNA/RNA kits and one RNA only kit were used. Sample extracts were evaluated on nucleic acid concentration, TapeStation DNA or RNA Integrity Number values and presence of PCR inhibitors. For the DNA kits, PFP produced higher concentrations compared with PLM and RPM, while MWFM gave higher DNA Integrity Number values when compared with RPM. No PCR inhibition was detected. For the RNA kits, RPM gave higher concentrations compared with MWTV and no differences were seen in RNA Integrity Number values. PCR inhibition was observed in all RNA samples, with MWTV exhibiting higher inhibition compared with RPM.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142248665","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 : 2024-09-13DOI: 10.1080/07366205.2024.2397288
Sonia Mukherjee,Pierre Leblanc,Mark C Poznansky,Ann E Sluder
{"title":"A HABA dye-based colorimetric assay to detect unoccupied biotin binding sites in an avidin-containing fusion protein.","authors":"Sonia Mukherjee,Pierre Leblanc,Mark C Poznansky,Ann E Sluder","doi":"10.1080/07366205.2024.2397288","DOIUrl":"https://doi.org/10.1080/07366205.2024.2397288","url":null,"abstract":"Avidin-biotin binding, the most robust non-covalent protein-ligand interaction occurring in nature, has wide-ranging applications in biotechnology. A frequent challenge in these applications is accurately determining the number of unoccupied biotin binding sites in avidin-containing fusion proteins. We delineate a novel assay protocol in miniaturized format to quantify available biotin binding sites based on the affinity of the anionic dye 4'-hydroxyazobenzene-2-carboxylic acid for biotin binding sites within avidin. We apply this assay as a quality control assay to evaluate the number of available biotin binding sites in different fusion protein production batches. This method offers a streamlined alternative to fluorescence-based assays commonly employed to assess biotin binding, is less time-consuming than other methods and is applicable to diverse fusion proteins.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142248664","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}
{"title":"An automatic classification method of testicular histopathology based on SC-YOLO framework.","authors":"Jinggen Wu,Yao Sun,Yangbo Jiang,Yangcheng Bu,Chong Chen,Jingping Li,Lejun Li,Weikang Chen,Keren Cheng,Jian Xu","doi":"10.1080/07366205.2024.2393544","DOIUrl":"https://doi.org/10.1080/07366205.2024.2393544","url":null,"abstract":"The pathological diagnosis and treatment of azoospermia depend on precise identification of spermatogenic cells. Traditional methods are time-consuming and highly subjective due to complexity of Johnsen score, posing challenges for accurately diagnosing azoospermia. Here, we introduce a novel SC-YOLO framework for automating the classification of spermatogenic cells that integrates S3Ghost module, CoordAtt module and DCNv2 module, effectively capturing texture and shape features of spermatogenic cells while reducing model parameters. Furthermore, we propose a simplified Johnsen score criteria to expedite the diagnostic process. Our SC-YOLO framework presents the higher efficiency and accuracy of deep learning technology in spermatogenic cell recognition. Future research endeavors will focus on optimizing the model's performance and exploring its potential for clinical applications.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142223432","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 : 2024-09-12DOI: 10.1080/07366205.2024.2387993
Shapour Jalilzadeh,Valerie Walker,Gary P Leggatt,Eli Hatchwell
{"title":"When is an SNP not an SNP?","authors":"Shapour Jalilzadeh,Valerie Walker,Gary P Leggatt,Eli Hatchwell","doi":"10.1080/07366205.2024.2387993","DOIUrl":"https://doi.org/10.1080/07366205.2024.2387993","url":null,"abstract":"Genomic duplications are important sources of structural change and gene innovation. In humans, the most recent and highly identical sequences (>90% homology, >1 kb long) are known as segmental duplications (SDs). Single-nucleotide variants or single-nucleotide polymorphisms within SDs have not been systematically assessed due to limitations around mapping short-read sequencing data. Single-nucleotide variant rs62486260 was flagged in a study of familial renal stone disease but it was unclear whether it was real or an artifact resulting from the presence of a SD. We describe in silico and wet-lab approaches to investigate this, using segment-specific long-PCR assays, followed by short PCR for Sanger sequencing. Our conclusion was that rs62486260 is an artifact. Our approach can be generalized to deal with other such situations.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142223434","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 : 2024-09-12DOI: 10.1080/07366205.2024.2372939
Xinyan Wei,Xuezheng Ma,Feng Tian,Zhaohui Wei,Liping Zhang,Kongxin Hu
{"title":"Sampling and analysis methods of air-borne microorganisms in hospital air: a review.","authors":"Xinyan Wei,Xuezheng Ma,Feng Tian,Zhaohui Wei,Liping Zhang,Kongxin Hu","doi":"10.1080/07366205.2024.2372939","DOIUrl":"https://doi.org/10.1080/07366205.2024.2372939","url":null,"abstract":"Pathogenic microorganisms can spread in the air as bioaerosols. When the human body is exposed to different bioaerosols, various infectious diseases may occur. As indoor diagnosis and treatment environments, hospitals are relatively closed and have a large flow rate of people. This indoor environment contains complex aerosol components; therefore, effective sampling and detection of microbial elements are essential in airborne pathogen monitoring. This article reviews the sampling and detection of different kinds of microorganisms in bioaerosols from indoor diagnostic and therapeutic settings, with a particular focus on microbial activity. This provides deeper insights into bioaerosols in diagnostic and therapeutic settings.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142177492","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}
{"title":"Mito-kaede photoactivation and chase experiment for mitophagy: optimizing flux measurement via fluid exchange system.","authors":"Hiroyuki Morinaga,Yoh Sugawara,Yoshinori Kitagawa,Jingyuan Chen,Nobuo Yasuda,Hiroki Ogata,Yoshihiro Yamaguchi,Masao Kaneki,Joseph A Jeevendra Martyn,Shingo Yasuhara","doi":"10.1080/07366205.2024.2372955","DOIUrl":"https://doi.org/10.1080/07366205.2024.2372955","url":null,"abstract":"Modulating autophagy and mitophagy, vital cellular quality control systems, offer therapeutic potential for critical illnesses. However, limited drug screening options hinder progress. We present a novel assay using the photoswitchable fluorescent reporter, mito-Kaede, to quantify mitophagy flux. Mito-Kaede's superior UV-induced photoconversion and brightness post-conversion make it ideal for prolonged mitochondrial dynamics tracking. Its specificity in responding to mitophagy, confirmed by parkin-knockout cells, adds value. When coupled with a custom fluid exchange system, enabling efficient medium changes, precise mitophagy observations become feasible. This mitophagy assay, alongside our methodological insights, can decipher mitophagy's role in pathology and supports drug screening efforts.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142177493","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 : 2024-06-05DOI: 10.1080/07366205.2024.2348347
Heguo Ding, Yue Xu, Fei Fang, Hong Wang, Anqi Chen
{"title":"Functionalized primer initiated signal cycles and personal glucose meter for sensitive and portable miRNA analysis","authors":"Heguo Ding, Yue Xu, Fei Fang, Hong Wang, Anqi Chen","doi":"10.1080/07366205.2024.2348347","DOIUrl":"https://doi.org/10.1080/07366205.2024.2348347","url":null,"abstract":"","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141383309","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 : 2024-06-05DOI: 10.1080/07366205.2024.2352277
Vahid Khalaj, S. AghaAmiri, Sukhen C. Ghosh, Servando Hernandez Vargas, Majid Momeny, A. Azhdarinia
{"title":"A simple and rapid\u0000 in vitro\u0000 assay for identification of direct inhibitors of O\u0000 6\u0000 -methylguanine-DNA methyltransferase","authors":"Vahid Khalaj, S. AghaAmiri, Sukhen C. Ghosh, Servando Hernandez Vargas, Majid Momeny, A. Azhdarinia","doi":"10.1080/07366205.2024.2352277","DOIUrl":"https://doi.org/10.1080/07366205.2024.2352277","url":null,"abstract":"","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141385062","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}