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Extracting high-quality RNA from formaldehyde-fixed naturally aged neuromusculoskeletal tissues. 从甲醛固定的天然老化神经肌肉骨骼组织中提取高质量 RNA。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-04-01 Epub Date: 2024-02-09 DOI: 10.2144/btn-2023-0092
Seth D Thompson, Rajeswari Pichika, Richard L Lieber, Mitra Lavasani
{"title":"Extracting high-quality RNA from formaldehyde-fixed naturally aged neuromusculoskeletal tissues.","authors":"Seth D Thompson, Rajeswari Pichika, Richard L Lieber, Mitra Lavasani","doi":"10.2144/btn-2023-0092","DOIUrl":"10.2144/btn-2023-0092","url":null,"abstract":"<p><p>Modern approaches to discovering molecular mechanisms and validating treatments for age-related neuromusculoskeletal dysfunction typically rely on high-throughput transcriptome analysis. Previously harvested and fixed tissues offer an incredible reservoir of untapped molecular information. However, obtaining RNA from such formaldehyde-fixed neuromusculoskeletal tissues, especially fibrotic aged tissues, is technically challenging and often results in RNA degradation, chemical modification and yield reduction, prohibiting further analysis. Therefore, we developed a protocol to extract high-quality RNA from formaldehyde-fixed brain, cartilage, muscle and peripheral nerve isolated from naturally aged mice. Isolated RNA produced reliable gene expression data comparable to fresh and flash-frozen tissues and was sensitive enough to detect age-related changes, making our protocol valuable to researchers in the field of aging.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"153-160"},"PeriodicalIF":2.7,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10988388/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139705987","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
Recording the brain in vivo: emerging technologies for the exploration of mental health conditions. 活体记录大脑：探索精神健康状况的新兴技术。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-04-01 Epub Date: 2024-03-14 DOI: 10.2144/btn-2024-0013
Tristan Free
{"title":"Recording the brain <i>in vivo</i>: emerging technologies for the exploration of mental health conditions.","authors":"Tristan Free","doi":"10.2144/btn-2024-0013","DOIUrl":"10.2144/btn-2024-0013","url":null,"abstract":"<p><p>Standfirst Mounting interest in mental health conditions over the last two decades has been coupled with the increasing sophistication of techniques to study the brain <i>in vivo</i>. [Formula: see text].</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"121-124"},"PeriodicalIF":2.7,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140118685","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 optimal genomic DNA extraction method for shoots of four Dendrocalamus species based on membership function analysis. 基于成员函数分析的四种 Dendrocalamus 树种嫩枝基因组 DNA 最佳提取方法。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-03-01 Epub Date: 2023-12-22 DOI: 10.2144/btn-2023-0087
Yingchun Ma, Bowen Li, Dejia Yang, Shuguang Wang, Lixia Yu, Hui Zhan, Juan Li
{"title":"An optimal genomic DNA extraction method for shoots of four <i>Dendrocalamus</i> species based on membership function analysis.","authors":"Yingchun Ma, Bowen Li, Dejia Yang, Shuguang Wang, Lixia Yu, Hui Zhan, Juan Li","doi":"10.2144/btn-2023-0087","DOIUrl":"10.2144/btn-2023-0087","url":null,"abstract":"<p><p>High-quality genomic DNA extraction is fundamental for the study of gene cloning and expression in plants. Therefore, this study evaluated several methods for extracting genomic DNA from shoots of four <i>Dendrocalamus</i> species to determine the optimal technique. Genomic DNA was extracted using three different methods: a commercial DNA extraction kit method, a modified cetyltrimethylammonium bromide method and a sodium dodecyl sulfate method. A membership function analysis was employed to compare these methods. The results demonstrated that the commercial DNA extraction kit method was the most effective and comprehensive approach for extracting genomic DNA from shoots of four <i>Dendrocalamus</i> species. Furthermore, this study provided valuable insights into optimizing techniques for extracting genomic DNA in other bamboo species.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"94-103"},"PeriodicalIF":2.7,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138828137","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
Corrigendum. 更正。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-03-01 Epub Date: 2024-02-28 DOI: 10.2144/btn-2020-0153c1
{"title":"Corrigendum.","authors":"","doi":"10.2144/btn-2020-0153c1","DOIUrl":"10.2144/btn-2020-0153c1","url":null,"abstract":"","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"119"},"PeriodicalIF":2.7,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139982268","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
Corrigendum. 更正。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-03-01 Epub Date: 2024-02-28 DOI: 10.2144/btn-2022-0032c1
{"title":"Corrigendum.","authors":"","doi":"10.2144/btn-2022-0032c1","DOIUrl":"10.2144/btn-2022-0032c1","url":null,"abstract":"","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"120"},"PeriodicalIF":2.7,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139982269","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
Assessment of measurement accuracy of amplified DNA using a colorimetric loop-mediated isothermal amplification assay. 使用比色环介导等温扩增检测法评估扩增 DNA 的测量精度。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-03-01 Epub Date: 2023-12-22 DOI: 10.2144/btn-2023-0104
Seongsoo Hong, Jeongho Park, Jaekyung Bok, Euna Cho, Joowon Rhee
{"title":"Assessment of measurement accuracy of amplified DNA using a colorimetric loop-mediated isothermal amplification assay.","authors":"Seongsoo Hong, Jeongho Park, Jaekyung Bok, Euna Cho, Joowon Rhee","doi":"10.2144/btn-2023-0104","DOIUrl":"10.2144/btn-2023-0104","url":null,"abstract":"<p><p>A colorimetric loop-mediated isothermal amplification assay detects changes in pH during amplification based on color changes at a constant temperature. Currently, various studies have focused on developing and assessing molecular point-of-care testing instruments. In this study, we evaluated amplified DNA concentrations measured using the colorimetric LAMP assay of the 1POT™ Professional device (1drop Inc, Korea). Results of the 1POT analysis of clinical samples were compared with measurements obtained from the Qubit™ 4 and NanoDrop™ 2000 devices (both from Thermo Fisher Scientific, MA, USA). These results showed a correlation of 0.98 (95% CI: 0.96-0.99) and 0.96 (95% CI: 0.92-0.98) between 1POT and the Qubit and NanoDrop. 1POT can measure amplified DNA accurately and is suitable for on-site molecular diagnostics.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"114-118"},"PeriodicalIF":2.7,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138828138","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 novel method for sampling subgingival microbiome: a comparative metatranscriptomic study. 龈下微生物组取样的新方法：一项元转录组学比较研究。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-03-01 Epub Date: 2024-02-06 DOI: 10.2144/btn-2023-0076
Diana Demusaj, Ryan Toma, Tanveer Khan, Lan Hu, Guruduth Banavar, Momchilo Vuyisich
{"title":"A novel method for sampling subgingival microbiome: a comparative metatranscriptomic study.","authors":"Diana Demusaj, Ryan Toma, Tanveer Khan, Lan Hu, Guruduth Banavar, Momchilo Vuyisich","doi":"10.2144/btn-2023-0076","DOIUrl":"10.2144/btn-2023-0076","url":null,"abstract":"<p><p>The subgingival microbiome has been implicated in oral and systemic diseases such as periodontitis and Alzheimer's disease. However, subgingival sampling is challenging. We developed a novel method of sampling the subgingival microbiome by rotationally swabbing the supragingival area, named subgingival-P (for proxy) samples. We sampled and metatranscriptomically analyzed subgingival and subgingival-P samples of three different teeth in 20 individuals. The subgingival-P samples were comparable to the subgingival samples in the relative abundances of microorganisms and microbial gene expression levels. Our data demonstrate that the novel method of collecting and analyzing the subgingival-P samples can act as a proxy for the subgingiva, paving the way for large and diverse studies investigating the role of the subgingival microbiome in health and disease.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"83-93"},"PeriodicalIF":2.7,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691151","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
Age is just a number: can proteomic analysis provide insight into the aging body? 年龄只是一个数字：蛋白质组分析能否让人了解人体的衰老？
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-03-01 Epub Date: 2024-02-22 DOI: 10.2144/btn-2024-0008
Jenny Straiton
{"title":"Age is just a number: can proteomic analysis provide insight into the aging body?","authors":"Jenny Straiton","doi":"10.2144/btn-2024-0008","DOIUrl":"10.2144/btn-2024-0008","url":null,"abstract":"<p><p>Recent proteomic studies have increased our understanding of the molecular process of aging, potentially enabling age-related diseases to be treated before the appearance of symptoms. [Formula: see text].</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"81-82"},"PeriodicalIF":2.7,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139929907","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
PS4: a next-generation dataset for protein single-sequence secondary structure prediction. PS4:下一代蛋白质单序列二级结构预测数据集。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-02-01 Epub Date: 2023-11-24 DOI: 10.2144/btn-2023-0024
Omar Peracha
{"title":"PS4: a next-generation dataset for protein single-sequence secondary structure prediction.","authors":"Omar Peracha","doi":"10.2144/btn-2023-0024","DOIUrl":"10.2144/btn-2023-0024","url":null,"abstract":"<p><p>Protein secondary structure prediction is a subproblem of protein folding. A light-weight algorithm capable of accurately predicting secondary structure from only the protein residue sequence could provide useful input for tertiary structure prediction, alleviating the reliance on multiple sequence alignments typically seen in today's best-performing models. Unfortunately, existing datasets for secondary structure prediction are small, creating a bottleneck. We present PS4, a dataset of 18,731 nonredundant protein chains and their respective secondary structure labels. Each chain is identified, and the dataset is nonredundant against other secondary structure datasets commonly seen in the literature. We perform ablation studies by training secondary structure prediction algorithms on the PS4 training set and obtains state-of-the-art accuracy on the CB513 test set in zero shots.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"63-70"},"PeriodicalIF":2.7,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138298252","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
Is space the final frontier for mitochondrial study? 太空是线粒体研究的最终前沿吗？
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-02-01 Epub Date: 2023-12-12 DOI: 10.2144/btn-2023-0071
Kit Neikirk, Dominique C Stephens, Heather K Beasley, Andrea G Marshall, Jennifer A Gaddy, Steven M Damo, Antentor Hinton
{"title":"Is space the final frontier for mitochondrial study?","authors":"Kit Neikirk, Dominique C Stephens, Heather K Beasley, Andrea G Marshall, Jennifer A Gaddy, Steven M Damo, Antentor Hinton","doi":"10.2144/btn-2023-0071","DOIUrl":"10.2144/btn-2023-0071","url":null,"abstract":"<p><p>Tweetable abstract This perspective considers several avenues for future research on mitochondrial dynamics, stress, and DNA in outer space.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"46-51"},"PeriodicalIF":2.7,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138797429","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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