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Methods in molecular biology最新文献

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Correction to: Characterization of the Mitochondria Function and Metabolism in Skin Fibroblasts Using the Biolog MitoPlate S-1. 更正：使用生物学线粒体板S-1表征皮肤成纤维细胞的线粒体功能和代谢。
Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4264-1_16
Alexandra C de Lemos, José Teixeira, Teresa Cunha-Oliveira
{"title":"Correction to: Characterization of the Mitochondria Function and Metabolism in Skin Fibroblasts Using the Biolog MitoPlate S-1.","authors":"Alexandra C de Lemos, José Teixeira, Teresa Cunha-Oliveira","doi":"10.1007/978-1-0716-4264-1_16","DOIUrl":"https://doi.org/10.1007/978-1-0716-4264-1_16","url":null,"abstract":"","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2878 ","pages":"C1"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Correction to: Combining Oligo Pools and Golden Gate Cloning to Create Protein Variant Libraries or Guide RNA Libraries for CRISPR Applications. 更正：结合Oligo池和金门克隆创建用于CRISPR应用的蛋白质变体文库或向导RNA文库。
Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4220-7_28
Alicia Maciá Valero, Rianne C Prins, Thijs de Vroet, Sonja Billerbeck
{"title":"Correction to: Combining Oligo Pools and Golden Gate Cloning to Create Protein Variant Libraries or Guide RNA Libraries for CRISPR Applications.","authors":"Alicia Maciá Valero, Rianne C Prins, Thijs de Vroet, Sonja Billerbeck","doi":"10.1007/978-1-0716-4220-7_28","DOIUrl":"https://doi.org/10.1007/978-1-0716-4220-7_28","url":null,"abstract":"","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2850 ","pages":"C1"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142979127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Deep Learning and PSSM Profile Approach for Accurate SNARE Protein Prediction. 基于深度学习和PSSM谱的陷阱蛋白准确预测方法。
Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4314-3_5
Quang Hien Kha, Huu Phuc Lam Nguyen, Nguyen Quoc Khanh Le
{"title":"A Deep Learning and PSSM Profile Approach for Accurate SNARE Protein Prediction.","authors":"Quang Hien Kha, Huu Phuc Lam Nguyen, Nguyen Quoc Khanh Le","doi":"10.1007/978-1-0716-4314-3_5","DOIUrl":"https://doi.org/10.1007/978-1-0716-4314-3_5","url":null,"abstract":"<p><p>SNARE proteins play a pivotal role in membrane fusion and various cellular processes. Accurate identification of SNARE proteins is crucial for elucidating their functions in both health and disease contexts. This chapter presents a novel approach employing multiscan convolutional neural networks (CNNs) combined with position-specific scoring matrix (PSSM) profiles to accurately recognize SNARE proteins. By leveraging deep learning techniques, our method significantly enhances the accuracy and efficacy of SNARE protein classification. We detail the step-by-step methodology, including dataset preparation, feature extraction using PSI-BLAST, and the design of the multiscan CNN architecture. Our results demonstrate that this approach outperforms existing methods, providing a robust and reliable tool for bioinformatics research.</p>","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2887 ","pages":"79-89"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142979129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bimolecular Fluorescence Complementation (BiFC) Technique for Exocytic Proteins in Murine Hippocampal Neurons. 小鼠海马神经元胞外蛋白的双分子荧光互补技术。
Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4314-3_20
Gözdem Karapinar Kapucu, Thorsten Trimbuch, Christian Rosenmund, Marion Weber-Boyvat
{"title":"Bimolecular Fluorescence Complementation (BiFC) Technique for Exocytic Proteins in Murine Hippocampal Neurons.","authors":"Gözdem Karapinar Kapucu, Thorsten Trimbuch, Christian Rosenmund, Marion Weber-Boyvat","doi":"10.1007/978-1-0716-4314-3_20","DOIUrl":"https://doi.org/10.1007/978-1-0716-4314-3_20","url":null,"abstract":"<p><p>The bimolecular fluorescence complementation (BiFC) technique is a powerful tool for visualizing protein-protein interactions in vivo. It involves genetically fused nonfluorescent fragments of green fluorescent protein (GFP) or its variants to the target proteins of interest. When these proteins interact, the GFP fragments come together, resulting in the reconstitution of a functional fluorescent protein complex that can be observed using fluorescence microscopy. In this chapter, we provide a detailed overview of the BiFC method and its application in studying protein-protein interactions in mouse hippocampal neurons. We discuss experimental procedures, including virus construct design, neuronal transduction, and imaging optimization. Additionally, we explore complementary assays for result validation and address potential challenges associated with BiFC experiments in the neuronal system. Overall, the BiFC offers researchers a valuable approach for investigating the spatial and temporal dynamics of protein interactions in living neuronal cells.</p>","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2887 ","pages":"281-294"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142979136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Quality Assurance in Metabolomics and Metabolic Profiling. 代谢组学和代谢谱的质量保证。
Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4334-1_2
Jennifer A Kirwan, Ulrike Bruning, Jonathan D Mosley
{"title":"Quality Assurance in Metabolomics and Metabolic Profiling.","authors":"Jennifer A Kirwan, Ulrike Bruning, Jonathan D Mosley","doi":"10.1007/978-1-0716-4334-1_2","DOIUrl":"https://doi.org/10.1007/978-1-0716-4334-1_2","url":null,"abstract":"<p><p>Metabolic profiling (untargeted metabolomics) aims for a global unbiased analysis of metabolites in a cell or biological system. It remains a highly useful research tool used across various analytical platforms. Incremental improvements across multiple steps in the analytical process may have large consequences for the end quality of the data. Thus, this chapter concentrates on which aspects of quality assurance can be implemented by a lab in the (pre-)analytical stages of the analysis to improve the overall end quality of their data. The scope of this chapter is limited to liquid-chromatography-mass spectrometry (LC-MS)-based profiling, which is one of the most widely utilized platforms, although the general principles are applicable to all metabolomics experiments.</p>","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2891 ","pages":"15-51"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142984040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Untargeted Metabolic Phenotyping by LC-MS. LC-MS的非靶向代谢表型分析。
Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4334-1_6
Ian D Wilson, Elizabeth Want
{"title":"Untargeted Metabolic Phenotyping by LC-MS.","authors":"Ian D Wilson, Elizabeth Want","doi":"10.1007/978-1-0716-4334-1_6","DOIUrl":"https://doi.org/10.1007/978-1-0716-4334-1_6","url":null,"abstract":"<p><p>Untargeted analysis by LC-MS is a valuable tool for metabolic profiling (metabonomics/metabolomics), and applications of this technology have grown rapidly over the past decade. LC-MS offers advantages of speed, sensitivity, relative ease of sample preparation, and large dynamic range compared to other platforms in this role. However, like any analytical approach, there are still drawbacks and challenges that have to be overcome, some of which are being addressed by advances in both column chemistries and instrumentation. In particular, the combination of LC-MS with ion mobility offers many new possibilities for improved analyte separation, detection, and structural identification. There are many untargeted LC-MS approaches which can be applied to metabolic phenotyping, and these usually need to be optimized for the type of sample, the nature of the study, or the biological question. Some of the main LC-MS approaches for untargeted metabolic phenotyping are described in detail in the following protocol.</p>","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2891 ","pages":"109-129"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142984053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Purification and Ultramicroscopic Observation of the Influenza A Virus Ribonucleoprotein Complex.
Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4326-6_7
Masahiro Nakano, Takeshi Noda
{"title":"Purification and Ultramicroscopic Observation of the Influenza A Virus Ribonucleoprotein Complex.","authors":"Masahiro Nakano, Takeshi Noda","doi":"10.1007/978-1-0716-4326-6_7","DOIUrl":"https://doi.org/10.1007/978-1-0716-4326-6_7","url":null,"abstract":"<p><p>Influenza A virus (IAV) has an eight-segmented, single-stranded, negative-sense viral genomic RNA (vRNA). Each vRNA strand associates with nucleoproteins and an RNA-dependent RNA polymerase complex to form a viral ribonucleoprotein (vRNP) complex. IAV vRNPs adopt a flexible double-helical configuration that varies in length. Although the transcription and replication of vRNA take place in the context of vRNPs, the precise structural conformation of vRNPs during RNA synthesis remains partially elucidated. To unravel the intricate ultrastructure of the vRNP, it is necessary to purify it while preserving its native functionality. Herein, we introduce a comprehensive protocol for the purification of IAV vRNPs using glycerol gradient ultracentrifugation. Furthermore, we provide a method for the high-speed atomic force microscopy observation of vRNPs during viral RNA synthesis.</p>","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2890 ","pages":"141-149"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143074847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Live-Cell Single-Molecule Imaging of Influenza A Virus-Receptor Interaction.
Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4326-6_4
Lukas Broich, Yang Fu, Christian Sieben
{"title":"Live-Cell Single-Molecule Imaging of Influenza A Virus-Receptor Interaction.","authors":"Lukas Broich, Yang Fu, Christian Sieben","doi":"10.1007/978-1-0716-4326-6_4","DOIUrl":"https://doi.org/10.1007/978-1-0716-4326-6_4","url":null,"abstract":"<p><p>Influenza A viruses are a major health care burden, and their biology has been intensely studied for decades. However, many details of virus infection are still elusive, requiring the development of refined and advanced technologies. Super-resolution microscopy allows the study of virus replication at the scale of an infecting virus, offering an exciting perspective on previously unseen mechanistic details of infection. Here we describe the materials and procedures required to perform single-molecule imaging of virus-receptor interaction in live cells. We further provide hints and tips on how to analyze and visualize the obtained datasets.</p>","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2890 ","pages":"89-101"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143074559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Purification and Reconstitution of Ilyobacter tartaricus ATP Synthase. 酒石酸伊杆菌ATP合酶的纯化与重组。
Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4280-1_3
Ganna O Krasnoselska, Thomas Meier
{"title":"Purification and Reconstitution of Ilyobacter tartaricus ATP Synthase.","authors":"Ganna O Krasnoselska, Thomas Meier","doi":"10.1007/978-1-0716-4280-1_3","DOIUrl":"10.1007/978-1-0716-4280-1_3","url":null,"abstract":"<p><p>F-type Adenosine triphosphate (ATP) synthase is a membrane-bound macromolecular complex, which is responsible for the synthesis of ATP, the universal energy source in living cells. This enzyme uses the proton- or sodium-motive force to power ATP synthesis by a unique rotary mechanism and can also operate in reverse, ATP hydrolysis, to generate ion gradients across membranes. The F<sub>1</sub>F<sub>o</sub>-ATP synthases from bacteria consist of eight different structural subunits, forming a complex of ~550 kDa in size. In the bacterium Ilyobacter tartaricus, the ATP synthase has the stoichiometry α<sub>3</sub>β<sub>3</sub>γδεab<sub>2</sub>c<sub>11</sub>. This chapter describes a wet-lab working protocol for the purification of several tens of milligrams of pure, heterologously (E. coli-) produced I. tartaricus Na<sup>+</sup>-driven F<sub>1</sub>F<sub>o</sub>-ATP synthase and its subsequent efficient reconstitution into proteoliposomes. The methods are useful for a broad range of subsequent biochemical and biotechnological applications.</p>","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2881 ","pages":"65-86"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Current Perspective of Medical Informatics Developments for a Clinical Translation of (Non-coding)RNAs and Single-Cell Technologies. 非编码）RNA 和单细胞技术临床转化的医学信息学发展现状透视》（A Current Perspective of Medical Informatics Developments for a Clinical Translation of (Non-coding)RNAs and Single-Cell Technologies）。
Methods in molecular biology Pub Date : 2025-01-01 DOI: 10.1007/978-1-0716-4290-0_2
Alexandra Baumann, Najia Ahmadi, Markus Wolfien
{"title":"A Current Perspective of Medical Informatics Developments for a Clinical Translation of (Non-coding)RNAs and Single-Cell Technologies.","authors":"Alexandra Baumann, Najia Ahmadi, Markus Wolfien","doi":"10.1007/978-1-0716-4290-0_2","DOIUrl":"10.1007/978-1-0716-4290-0_2","url":null,"abstract":"<p><p>The journey from laboratory research to clinical practice is marked by significant advancements in the fields of single-cell technologies and non-coding RNA (ncRNA) research. This convergence may reshape our approach to personalized medicine, offering groundbreaking insights and treatments in various clinical settings. This chapter discusses advancements in (nc)RNAs in the clinics, innovations in single-cell technologies and algorithms, and the impact on actual precision medicine, showing the integration of single-cell and ncRNA research can have a tangible impact on precision medicine. Case studies in Oncology, Immunology, and other fields demonstrate how these technologies can guide treatment decisions, tailor therapies to individual patients, and improve outcomes. This approach is particularly potent in addressing diseases with high inter- and intra-tumor heterogeneity. The final sections address standardization, data integration, and analysis challenges because the complexity and volume of data generated by single-cell and ncRNA research poses significant challenges. Medical Informatics is not just a support tool but could be seen as a pivotal component in advancing clinical applications of single-cell and ncRNA research by bridging the gap between bench and bedside. The future of personalized medicine depends on our ability to harness the power of these technologies, and Medical Informatics in combination with ncRNA and single-cell technologies may stand at the forefront of this endeavor.</p>","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2883 ","pages":"31-51"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","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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