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Welcome to the 76th Issue of BioTechniques. 欢迎阅读第 76 期《生物技术》。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-01-01 DOI: 10.2144/btn-2023-0113
Ashling Cannon, Ebony Torrington, Tristan Free
{"title":"Welcome to the 76th Issue of <i>BioTechniques</i>.","authors":"Ashling Cannon, Ebony Torrington, Tristan Free","doi":"10.2144/btn-2023-0113","DOIUrl":"10.2144/btn-2023-0113","url":null,"abstract":"","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"76 1","pages":"1-4"},"PeriodicalIF":2.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139429539","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
Prioritizing privacy and presentation of supportable hypothesis testing in forensic genetic genealogy investigations. 在法医遗传系谱调查中优先考虑隐私和提出可支持的假设检验。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-01-01 Epub Date: 2024-08-09 DOI: 10.1080/07366205.2024.2386218
Bruce Budowle, Lee Baker, Antti Sajantila, Kristen Mittelman, David Mittelman
{"title":"Prioritizing privacy and presentation of supportable hypothesis testing in forensic genetic genealogy investigations.","authors":"Bruce Budowle, Lee Baker, Antti Sajantila, Kristen Mittelman, David Mittelman","doi":"10.1080/07366205.2024.2386218","DOIUrl":"10.1080/07366205.2024.2386218","url":null,"abstract":"<p><p>Investigative leads are not generated by traditional forensic DNA testing, if the source of the forensic evidence or a 1st degree relative of unidentified human remains is not in the DNA database. In such cases, forensic genetic genealogy (FGG) can provide valuable leads. However, FGG generated genetic data contain private and sensitive information. Therefore, it is essential to deploy approaches that minimize unnecessary disclosure of these data to mitigate potential risks to individual privacy. We recommend protective practices that need not impact effective reporting of relationship identifications. Examples include performing one-to-one comparisons of DNA profiles of third-party samples and evidence samples offline with an \"air gap\" to the internet and shielding the specific shared single nucleotide polymorphisms (SNP) states and locations by binning adjacent SNPs in forensic reports. Such approaches reduce risk of unwanted access to or reverse engineering of third-party individuals' genetic data and can give these donors greater confidence to support use of their DNA profiles in FGG investigation.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"425-431"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141905820","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
Mapping the spread of antibiotic resistance genes in the coastal microbiome. 绘制沿海微生物群中抗生素耐药性基因的传播图。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-01-01 Epub Date: 2024-10-21 DOI: 10.1080/07366205.2024.2416379
Jasmine Hagan
{"title":"Mapping the spread of antibiotic resistance genes in the coastal microbiome.","authors":"Jasmine Hagan","doi":"10.1080/07366205.2024.2416379","DOIUrl":"10.1080/07366205.2024.2416379","url":null,"abstract":"<p><p>StandfirstCoastal environments are becoming increasingly exposed to antibiotics through anthropogenic inputs. But how could emerging metagenomic techniques be used to map the spread of antibiotic resistance genes in the coastal microbiome?[Formula: see text].</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"411-414"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142457180","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
Predicting molecular docking of per- and polyfluoroalkyl substances to blood protein using generative artificial intelligence algorithm DiffDock. 使用生成人工智能算法DiffDock预测全氟烷基和多氟烷基物质与血液蛋白质的分子对接。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-01-01 Epub Date: 2023-11-10 DOI: 10.2144/btn-2023-0070
Dhan Lord B Fortela, Ashley P Mikolajczyk, Miranda R Carnes, Wayne Sharp, Emmanuel Revellame, Rafael Hernandez, William E Holmes, Mark E Zappi
{"title":"Predicting molecular docking of per- and polyfluoroalkyl substances to blood protein using generative artificial intelligence algorithm DiffDock.","authors":"Dhan Lord B Fortela, Ashley P Mikolajczyk, Miranda R Carnes, Wayne Sharp, Emmanuel Revellame, Rafael Hernandez, William E Holmes, Mark E Zappi","doi":"10.2144/btn-2023-0070","DOIUrl":"10.2144/btn-2023-0070","url":null,"abstract":"<p><p>This study computationally evaluates the molecular docking affinity of various perfluoroalkyl and polyfluoroalkyl substances (PFAs) towards blood proteins using a generative machine-learning algorithm, DiffDock, specialized in protein-ligand blind-docking learning and prediction. Concerns about the chemical pathways and accumulation of PFAs in the environment and eventually in the human body has been rising due to empirical findings that levels of PFAs in human blood has been rising. DiffDock may offer a fast approach in determining the fate and potential molecular pathways of PFAs in human body.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"14-26"},"PeriodicalIF":2.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72013339","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
pJoseph2: a family of plasmids as positive controls for bacterial protein expression, transfections, and western blots. pJoseph2：质粒系列，可作为细菌蛋白质表达、转染和 Western 印迹的阳性对照。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-01-01 Epub Date: 2024-05-12 DOI: 10.1080/07366205.2024.2343609
Ebru Robinson, Elizabeth Barajas Alonso, Jennifer A Waters, Cayleen Bileckyj, Carrie D House, Christopher A Johnston, Richard M Cripps
{"title":"pJoseph2: a family of plasmids as positive controls for bacterial protein expression, transfections, and western blots.","authors":"Ebru Robinson, Elizabeth Barajas Alonso, Jennifer A Waters, Cayleen Bileckyj, Carrie D House, Christopher A Johnston, Richard M Cripps","doi":"10.1080/07366205.2024.2343609","DOIUrl":"10.1080/07366205.2024.2343609","url":null,"abstract":"<p><p>Epitope tagging represents a powerful strategy for expedited identification, isolation, and characterization of proteins in molecular biological studies, including protein-protein interactions. We aimed to improve the reproducibility of epitope-tagged protein expression and detection by developing a range of plasmids as positive controls. The pJoseph2 family of expression plasmids functions in diverse cellular environments and cell types to enable the evaluation of transfection efficiency and antibody staining for epitope detection. The expressed green fluorescent proteins harbor five unique epitope tags, and their efficient expression in <i>Escherichia coli</i>, <i>Drosophila</i> Schneider's line 2 cells, and human SKOV3 and HEK293T cells was demonstrated by fluorescence microscopy and western blotting. The pJoseph2 plasmids provide versatile and valuable positive controls for numerous experimental applications.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"76 7","pages":"299-309"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142054860","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
Automated method for quantification of 20 amino acids in cell culture media during biopharmaceutical development. 生物制药开发过程中细胞培养基中20种氨基酸的自动定量方法。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-01-01 Epub Date: 2023-11-24 DOI: 10.2144/btn-2023-0068
Ankita Dubey, Srishti Joshi, Kratika Upadhyay, Ansuman Mahato, Anurag S Rathore
{"title":"Automated method for quantification of 20 amino acids in cell culture media during biopharmaceutical development.","authors":"Ankita Dubey, Srishti Joshi, Kratika Upadhyay, Ansuman Mahato, Anurag S Rathore","doi":"10.2144/btn-2023-0068","DOIUrl":"10.2144/btn-2023-0068","url":null,"abstract":"<p><p>Herein, a step-by-step protocol for simultaneous detection of 20 amino acids commonly present in cell culture media is described. The protocol facilitates detection of both primary and secondary amino acids through a two-step precolumn derivatization strategy using ortho-phthalaldehyde and 9-fluorenylmethyl chloroformate as derivatizing agents. The separation of derivatized amino acids with varying hydrophobicity is achieved through reverse-phase chromatography. The amino acids are simultaneously detected in a single workflow through the use of Variable Wavelength Detector at 338 and 262 nm. The protocol is applicable for both mammalian and bacterial cell culture matrices with an option for automation of precolumn derivatization.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"27-36"},"PeriodicalIF":2.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138298251","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
Modular probe-based colorimetric miRNA detection via polymerase/endonuclease assisted chain displacement. 通过聚合酶/内切酶辅助链置换进行基于探针的模块化比色 miRNA 检测。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-01-01 Epub Date: 2024-07-23 DOI: 10.1080/07366205.2024.2368394
Xialing Xu, Ping Zhang, Siyu Tao
{"title":"Modular probe-based colorimetric miRNA detection <i>via</i> polymerase/endonuclease assisted chain displacement.","authors":"Xialing Xu, Ping Zhang, Siyu Tao","doi":"10.1080/07366205.2024.2368394","DOIUrl":"10.1080/07366205.2024.2368394","url":null,"abstract":"<p><p>Methods for sequence-specific microRNA (miRNA) analysis are crucial for miRNA research and guiding nursing strategies. We have devised a colorimetric technique for detecting miRNA using a dumbbell probe-based polymerase/endonuclease assisted chain displacement, along with silver ions (Ag<sup>+</sup>) aptamer assisted color reaction. The suggested approach enables precise measurement of miRNA-21 within the concentration range of 100 fM-5 nM, with a low detection limit of 45.32 fM. Additionally, it exhibits exceptional capability in distinguishing variations at the level of individual nucleotides. Furthermore, the detection technique may be utilized to precisely measure the amount of miRNA-21 in serum samples, demonstrating a high level of concordance with the findings obtained from a commercially available miRNA detection kit.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"371-379"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747399","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
Isothermal amplification of long DNA fragments at low temperature by improved strand displacement amplification. 通过改进的链置换扩增技术在低温下等温扩增长 DNA 片段。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-01-01 Epub Date: 2024-03-28 DOI: 10.2144/btn-2024-0012
Yinhua Zhang, Ashley N Luck, Nathan A Tanner
{"title":"Isothermal amplification of long DNA fragments at low temperature by improved strand displacement amplification.","authors":"Yinhua Zhang, Ashley N Luck, Nathan A Tanner","doi":"10.2144/btn-2024-0012","DOIUrl":"10.2144/btn-2024-0012","url":null,"abstract":"<p><p>Strand displacement amplification (SDA) is an isothermal amplification technique wherein amplification of a nucleic acid is initiated by nicking enzyme activity at sites flanking the target. Diagnostic SDA is very fast but requires precise optimization and is limited to very short amplicons. Here we report an enhanced approach by addition of single-stranded DNA binding protein, crowding agents and dUTP to enable amplification of kilobase-length products at low temperatures. Additionally, we pair this improved SDA with a novel carryover contamination prevention, eliminating amplifiable DNA at the end of the reaction to reduce contamination risk. Taken together these developments increase the utility and versatility of SDA, broadening the reach of this powerful but uncommonly used method.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"255-262"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140304764","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
Decoding disease: Scott Patterson's perspectives on the power of biomarkers in drug development. 解码疾病:斯科特·帕特森对药物开发中生物标志物力量的看法。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-01-01 Epub Date: 2023-11-23 DOI: 10.2144/btn-2023-0108
Scott D Patterson
{"title":"Decoding disease: Scott Patterson's perspectives on the power of biomarkers in drug development.","authors":"Scott D Patterson","doi":"10.2144/btn-2023-0108","DOIUrl":"10.2144/btn-2023-0108","url":null,"abstract":"<p><p>Scott Patterson (Gilead Sciences Inc., CA, USA) speaks to Ashling Cannon, Journal Development Editor at <i>BioTechniques</i>, about his career. Patterson is a biochemist and proteomics and biomarker/translational expert with over 30 years of industry experience following 13 years in an academic setting. Patterson earned his BSc and PhD in Physiology and Pharmacology from the University of Queensland (Australia) while working full time in the Department of Physiology and Pharmacology, rising to a Senior Research Officer. Throughout his career, Patterson has been actively involved in advancing technologies, how they can be applied to address biological questions and the interplay of bioinformatics and large datasets leveraging biomarkers and diagnostics. He has held pivotal roles at renowned institutions and companies such as Cold Spring Harbor Laboratory (NY, USA), Amgen, Inc. (CA, USA), Celera Genomics Group (MD, USA) and Gilead Sciences, Inc. Notably, he served as a Staff Investigator at Cold Spring Harbor Laboratory and was honored with the Long Island Biological Association New Investigator award in addition to being the 2002 Barnett Lecturer at Northeastern University (MA, USA). In early 2015 Patterson joined Gilead Sciences, Inc., bringing his extensive expertise to lead biomarker discovery and development as well as <i>in vitro</i> diagnostics initiatives across all therapeutic domains.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"9-13"},"PeriodicalIF":2.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138294493","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
Three-dimensional visualization and analysis of dendritic spines in human brain tissue. 人脑组织树突棘的三维可视化与分析。
IF 2.7 4区 工程技术
BioTechniques Pub Date : 2024-01-01 Epub Date: 2023-11-23 DOI: 10.2144/btn-2023-0078
Haitao Sun, Hei Ming Lai, Wutian Wu
{"title":"Three-dimensional visualization and analysis of dendritic spines in human brain tissue.","authors":"Haitao Sun, Hei Ming Lai, Wutian Wu","doi":"10.2144/btn-2023-0078","DOIUrl":"10.2144/btn-2023-0078","url":null,"abstract":"<p><p>We developed a simple yet powerful technique to visualize neuronal morphology in human brain tissues. By ballistically shooting DiI (1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate)-coated tungsten particles to randomly label neurons, then clearing tissues with OPTIClear, we demonstrated the tracing of branched dendritic trees and spines in three dimensions. High-resolution imaging revealed dendrites up to 300 μm long and spine necks down to 200 nm across. Quantitative analyses of 1304 dendritic spines showed no decrease in spine density with imaging depth, indicating excellent clearing and tracing. Segmentation and modeling of dendritic spines enabled morphological characterization. This technique enables assumption-free, high-resolution and cost-efficient visualization of neuronal morphology in human tissues. Combined with immunohistochemistry and electron microscopy, it could provide new perspectives for studying human neuroanatomy and pathology.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"37-42"},"PeriodicalIF":2.7,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138294494","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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