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A single-cell 3D dynamic volume control system for chondrocytes. 软骨细胞单细胞三维动态体积控制系统
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-10-15 DOI: 10.1080/07366205.2024.2412414
Qiang Zhang, Yiyao Wang, Yanjun Zhang, Xiaochun Wei, Weiyi Chen, Quanyou Zhang
{"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":" ","pages":"1-10"},"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}
引用次数: 0
Comparison of commercially available DNA and RNA extraction kits for wildlife feces collected from the environment. 针对从环境中收集的野生动物粪便的市售 DNA 和 RNA 提取试剂盒比较。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-09-13 DOI: 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":"1 1","pages":"1-10"},"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}
引用次数: 0
A HABA dye-based colorimetric assay to detect unoccupied biotin binding sites in an avidin-containing fusion protein. 基于 HABA 染料的比色测定法，用于检测含阿维丁融合蛋白中未被占用的生物素结合位点。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-09-13 DOI: 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":"22 1","pages":"1-10"},"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}
引用次数: 0
An automatic classification method of testicular histopathology based on SC-YOLO framework. 基于 SC-YOLO 框架的睾丸组织病理学自动分类方法。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-09-12 DOI: 10.1080/07366205.2024.2393544
Jinggen Wu,Yao Sun,Yangbo Jiang,Yangcheng Bu,Chong Chen,Jingping Li,Lejun Li,Weikang Chen,Keren Cheng,Jian Xu
{"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":"8 1","pages":"1-10"},"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}
引用次数: 0
When is an SNP not an SNP? 什么时候 SNP 不是 SNP？
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-09-12 DOI: 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":"10 1","pages":"1-9"},"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}
引用次数: 0
Sampling and analysis methods of air-borne microorganisms in hospital air: a review. 医院空气中气载微生物的采样和分析方法：综述。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-09-12 DOI: 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":"9 1","pages":"1-10"},"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}
引用次数: 0
Mito-kaede photoactivation and chase experiment for mitophagy: optimizing flux measurement via fluid exchange system. 有丝分裂的光激活和追逐实验：通过流体交换系统优化通量测量。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-09-11 DOI: 10.1080/07366205.2024.2372955
Hiroyuki Morinaga,Yoh Sugawara,Yoshinori Kitagawa,Jingyuan Chen,Nobuo Yasuda,Hiroki Ogata,Yoshihiro Yamaguchi,Masao Kaneki,Joseph A Jeevendra Martyn,Shingo Yasuhara
{"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":"1 1","pages":"1-13"},"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}
引用次数: 0
Using Longitudinal Variance Components Models to Assess Hyper-connectivity in Severe Traumatic Brain Injury Patients. 利用纵向变异成分模型评估严重脑损伤患者的超连接性。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-07-01 DOI: 10.32598/bcn.2022.3796.1
Keyvan Olazadeh, Nasrin Borumandnia, Mahin Habibi, Hamid Alavi Majd
{"title":"Using Longitudinal Variance Components Models to Assess Hyper-connectivity in Severe Traumatic Brain Injury Patients.","authors":"Keyvan Olazadeh, Nasrin Borumandnia, Mahin Habibi, Hamid Alavi Majd","doi":"10.32598/bcn.2022.3796.1","DOIUrl":"10.32598/bcn.2022.3796.1","url":null,"abstract":"<p><strong>Introduction: </strong>Traumatic brain injury (TBI) is one of the leading causes of death globally and one of the most important diseases indicated by the World Health Organization (WHO). Several studies have concluded that brain damage can dramatically increase functional connectivity (FC) in the brain. The effects of this hyper-connectivity are not yet fully understood and are being studied by neuroscientists. Accordingly, this study identifies areas of the brain where, after brain injury, an acute increase in FC in such areas is observed.</p><p><strong>Methods: </strong>The data used in this study were downloaded from the accessible open functional magnetic resonance imaging (fMRI) site. The data included fMRI of 14 patients with severe TBI and 12 healthy individuals. The longitudinal model of variance components investigated the difference between FC in the baseline effect and the longitudinal trend between the TBI and control groups.</p><p><strong>Results: </strong>After fitting the longitudinal model of variance components, no difference was observed between the FC of the two groups due to the baseline effect. However, in the longitudinal trend of FC, there was a statistically significant difference between the three pairs of cerebellum left, cerebellum right, superior frontal gyrus left, superior frontal gyrus right, thalamus left, and thalamus right in the TBI group compared to the control group.</p><p><strong>Conclusion: </strong>The results showed that FC was sharply increased in 3 pairs of areas in people with TBI. This hyper-connectivity can affect individuals' cognitive functions, including motor and sensory functions. The exact extent of this effect is unclear and requires further investigation by neuroscientists.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"60 1 1","pages":"509-518"},"PeriodicalIF":2.2,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11565661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90203133","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
Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogenies. Phylobook：从分子系统进化论中显示、注释和提取序列的工具。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-05-03 DOI: 10.2144/btn-2023-0056
Jeffrey C Furlong, Peter D Darley, Wenjie Deng, James I Mullins, Roger E Bumgarner
{"title":"Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogenies.","authors":"Jeffrey C Furlong, Peter D Darley, Wenjie Deng, James I Mullins, Roger E Bumgarner","doi":"10.2144/btn-2023-0056","DOIUrl":"https://doi.org/10.2144/btn-2023-0056","url":null,"abstract":"As the volume of sequence data from variable pathogens increases, means of analyzing, annotating and extracting specific taxa for study becomes more difficult. To meet these challenges for datasets with hundreds to thousands of taxa, 'Phylobook' was developed. Starting with a sequence alignment file, Phylobook generates and displays phylogenetic trees adjacent to highlighter plots showing the position of mutations, and allows the user to identify lineages and recombinants, annotate and export selected subsets of sequences for downstream analysis. Accurate lineage assignment, which is difficult to automate, is aided using annotations created by different clustering methods. Phylobook provides web-based display combined with automated clustering and manual editing to allow for expert assessment and correction of lineage assignments and extraction for downstream analysis.","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"45 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140830012","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
Comparing robotic and manual injection methods in zebrafish embryos for high-throughput RNA silencing using CRISPR-RfxCas13d. 比较使用 CRISPR-RfxCas13d 在斑马鱼胚胎中进行高通量 RNA 沉默的机器人和人工注射方法。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-05-01 Epub Date: 2024-02-29 DOI: 10.2144/btn-2023-0062
Joaquin Abugattas-Nuñez Del Prado, Yi Ding, Jan de Sonneville, Kees-Jan van der Kolk, Miguel A Moreno-Mateos, Edward Málaga-Trillo, Herman P Spaink
{"title":"Comparing robotic and manual injection methods in zebrafish embryos for high-throughput RNA silencing using CRISPR-RfxCas13d.","authors":"Joaquin Abugattas-Nuñez Del Prado, Yi Ding, Jan de Sonneville, Kees-Jan van der Kolk, Miguel A Moreno-Mateos, Edward Málaga-Trillo, Herman P Spaink","doi":"10.2144/btn-2023-0062","DOIUrl":"10.2144/btn-2023-0062","url":null,"abstract":"<p><p>In this study, the authors compared the efficiency of automated robotic and manual injection methods for the CRISPR-RfxCas13d (CasRx) system for mRNA knockdown and Cas9-mediated DNA targeting in zebrafish embryos. They targeted the no tail (<i>TBXTA</i>) gene as a proof-of-principle, evaluating the induced embryonic phenotypes. Both Cas9 and CasRx systems caused loss of function phenotypes for <i>TBXTA</i>. Cas9 protein exhibited a higher percentage of severe phenotypes compared with mRNA, while CasRx protein and mRNA showed similar efficiency. Both robotic and manual injections demonstrated comparable phenotype percentages and mortality rates. The findings highlight the potential of RNA-targeting CRISPR effectors for precise gene knockdown and endorse automated microinjection at a speed of 1.0 s per embryo as a high-throughput alternative to manual methods.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"183-191"},"PeriodicalIF":2.7,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139989247","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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