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Simple and sensitive detection of Pseudomonas aeruginosa in neonatal infection based on a both-end blocked peroxidase-mimicking DNAzyme. 基于双端阻断过氧化物酶模拟 DNA 酶对新生儿感染铜绿假单胞菌进行简单灵敏的检测。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-01-01 Epub Date: 2024-05-20 DOI: 10.1080/07366205.2024.2348295
Dongyun Chen, Yicong Pan, Huan Yu, Xiaoxiang Chen
{"title":"Simple and sensitive detection of <i>Pseudomonas aeruginosa</i> in neonatal infection based on a both-end blocked peroxidase-mimicking DNAzyme.","authors":"Dongyun Chen, Yicong Pan, Huan Yu, Xiaoxiang Chen","doi":"10.1080/07366205.2024.2348295","DOIUrl":"https://doi.org/10.1080/07366205.2024.2348295","url":null,"abstract":"<p><p>Developing a simple and highly sensitive approach for <i>Pseudomonas aeruginosa</i> (<i>P. aeruginosa</i>) detection is crucial, as it is closely associated with various disorders, such as newborn infections. Nevertheless, few of techniques have the capability to accurately identify <i>P. aeruginosa</i> with a high level of sensitivity and significantly improved stability. The employment of the both-end blocked peroxidase-mimicking DNAzyme significantly diminished the interferences from background signals, so conferring the approach with a high degree of selectivity and reproducibility. The proposed method is demonstrated with exceptional discernment capacity in differentiating interfering microorganisms. The simplicity, elevated sensitivity and high discerning capability make the method a highly promising alternative instrument for pathogenic bacteria detection.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"76 7","pages":"323-332"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142054861","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
Cassava for the future: embryogenic liquid cultures suitable for new biotech techniques. 未来的木薯：适合新生物技术的胚胎液体培养物。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-01-01 Epub Date: 2024-10-16 DOI: 10.1080/07366205.2024.2393546
Beata Dedičová, Luis Augusto Becerra Lopez-Lavalle
{"title":"Cassava for the future: embryogenic liquid cultures suitable for new biotech techniques.","authors":"Beata Dedičová, Luis Augusto Becerra Lopez-Lavalle","doi":"10.1080/07366205.2024.2393546","DOIUrl":"10.1080/07366205.2024.2393546","url":null,"abstract":"<p><p>Cassava, a crop of importance for subsistence farming in Africa, Asia, and Latin America, has the potential to benefit from global economic integration as a versatile industrial resource. Enhancing cassava productivity is not just a matter of agricultural competitiveness but a crucial step toward ensuring many communities' food security and livelihoods. Given its high performance in marginal environments, where climate change poses threats, ensuring food security and livelihoods relies on rapidly adapting cassava. This study aimed to develop a protocol that swiftly transitions cassava embryogenic short-period liquid suspension cultures, facilitating the regeneration of genetically stable <i>in vitro</i> plants. The resulting protocol, with its potential to be a foundational component in future technologies employing various genome editing or genetic modification techniques, holds promise for the advancement of cassava biotechnology.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"453-461"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142457179","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 standardized protocol for sample preparation for scanning electron microscopy to visualize extrachromosomal DNA. 用于扫描电子显微镜观察染色体外 DNA 的样本制备标准化方案。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-01-01 Epub Date: 2024-06-19 DOI: 10.1080/07366205.2024.2346042
Jillann A Madren, Jingting Chen, William Dennis, Christina Ford, Kristen K White, Elizabeth Brunk
{"title":"A standardized protocol for sample preparation for scanning electron microscopy to visualize extrachromosomal DNA.","authors":"Jillann A Madren, Jingting Chen, William Dennis, Christina Ford, Kristen K White, Elizabeth Brunk","doi":"10.1080/07366205.2024.2346042","DOIUrl":"https://doi.org/10.1080/07366205.2024.2346042","url":null,"abstract":"<p><p>Extrachromosomal DNA (ecDNA) are circular DNA structures associated with cancer and drug resistance. One specific type, double minute (DM) chromosomes, has been studied since the 1960s using imaging techniques like cytogenetics and fluorescence microscopy. Specialized techniques such as atomic force microscopy (AFM) and scanning electron microscopy (SEM) offer micro to nano-scale visualization, but current sample preparation methods may not optimally preserve ecDNA structure. Our study introduces a systematic protocol using SEM for high-resolution ecDNA visualization. We have optimized the end-to-end procedure, providing a standardized approach to explore the circular architecture of ecDNA and address the urgent need for better understanding in cancer research.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":"76 7","pages":"311-321"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142054859","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
Integrity of RNA in long-term-stored cervical liquid-based cytology samples: implications for biomarker research. 长期储存的宫颈液基细胞学样本中 RNA 的完整性：对生物标记研究的影响。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-01-01 Epub Date: 2024-05-01 DOI: 10.2144/btn-2023-0112
Madeleine P J White, Andrew Stevenson, Hana Elasifer, Chris Davies, Kyriaki Nomikou, Kate Cuschieri, Sheila V Graham
{"title":"Integrity of RNA in long-term-stored cervical liquid-based cytology samples: implications for biomarker research.","authors":"Madeleine P J White, Andrew Stevenson, Hana Elasifer, Chris Davies, Kyriaki Nomikou, Kate Cuschieri, Sheila V Graham","doi":"10.2144/btn-2023-0112","DOIUrl":"10.2144/btn-2023-0112","url":null,"abstract":"<p><p>Biobanks of cervical screening (LBC) samples annotated with disease status are an invaluable resource to support the development of tools for the risk stratification of disease. Although there is growing interest in the assessment of RNA-based biomarkers, little is known on the suitability and durability of stored clinical samples (commonly used in cervical screening) to support RNA-based research. RNA was extracted from 260 stored LBC samples. Storage at -80°C or -25°C allowed isolation of sufficient RNA for further analysis. RNA was found to be substantially degraded according to Agilent Bioanalyser data. Despite this, RT-qPCR was successful in 95% samples tested. These data suggest that biobanked LBC samples are suitable for RNA-based assessment even if stored for up to 14 years.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"245-253"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140852647","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
Novel buffer for long-term preservation of DNA in biological material at room temperature. 用于在室温下长期保存生物材料中 DNA 的新型缓冲液。
IF 2.2 4区 工程技术
BioTechniques Pub Date : 2024-01-01 Epub Date: 2024-07-01 DOI: 10.1080/07366205.2024.2360813
Mohaimin Kasu, Peter G Ristow, Adria Michelle Burrows, Zafrir Kuplik, Mark J Gibbons, Maria E D'Amato
{"title":"Novel buffer for long-term preservation of DNA in biological material at room temperature.","authors":"Mohaimin Kasu, Peter G Ristow, Adria Michelle Burrows, Zafrir Kuplik, Mark J Gibbons, Maria E D'Amato","doi":"10.1080/07366205.2024.2360813","DOIUrl":"10.1080/07366205.2024.2360813","url":null,"abstract":"<p><p>The collection and preservation of biological material before DNA analysis is critical for inter alia biomedical research, medical diagnostics, forensics and biodiversity conservation. In this study, we evaluate an in-house formulated buffer called the Forensic DNA Laboratory-buffer (FDL-buffer) for preservation of biological material for long term at room temperature. Human saliva stored in the buffer for 8 years, human blood stored for 3 years and delicate animal tissues from the jellyfish <i>Pelagia noctiluca</i> comb jelly <i>Beroe</i> sp., stored for 4 and 6 years respectively consistently produced high-quality DNA. FDL-buffer exhibited compatibility with standard organic, salting out and spin-column extraction methods, making it versatile and applicable to a wide range of applications, including automation.</p>","PeriodicalId":8945,"journal":{"name":"BioTechniques","volume":" ","pages":"357-370"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141466005","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
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
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
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
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
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
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