Methods in molecular biology最新文献_第9页

Laser-Capture Microdissection Followed by ATAC-Seq. 激光捕获显微解剖，随后进行ATAC-Seq。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-5154-4_12

Celia L Hartmann, Joachim L Schultze, Marc D Beyer, Caterina Carraro

引用次数: 0

Low-Input Proteomics Protocols for Laser-Captured FFPE Samples with Orbitrap Astral DIA-MS. Orbitrap Astral DIA-MS激光捕获FFPE样品的低输入蛋白质组学协议。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-5154-4_8

Daniele Musiani, Alessandro Cuomo

引用次数: 0

Exploring Protein Interactomes Using TurboID-Directed Proximity Labeling and Mass Spectrometry. 使用turboid定向接近标记和质谱法探索蛋白质相互作用组。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-5142-1_17

Elvio Rodríguez Araya, Gonzalo Martínez Peralta, Lucila Attala, Victoria Boselli, Azul de Hernández, Julia Pinheiro Chagas da Cunha, Esteban Serra

{"title":"Exploring Protein Interactomes Using TurboID-Directed Proximity Labeling and Mass Spectrometry.","authors":"Elvio Rodríguez Araya, Gonzalo Martínez Peralta, Lucila Attala, Victoria Boselli, Azul de Hernández, Julia Pinheiro Chagas da Cunha, Esteban Serra","doi":"10.1007/978-1-0716-5142-1_17","DOIUrl":"10.1007/978-1-0716-5142-1_17","url":null,"abstract":"Proximity labeling (PL) with TurboID provides a powerful alternative to traditional protein interaction mapping methods, allowing the capture of both stable and transient interactions in living cells. Here, we describe a standardized and optimized protocol for generating high-confidence proximity proteomes in Trypanosoma cruzi using a novel vector system, pTcTurboID. This vector allows the stable and regulatable expression of TurboID fusion proteins, ensuring minimal bait expression to preserve physiological function while maintaining sufficient biotinylation activity for protein detection. The protocol comprises eight steps, including the generation of spatial control and bait lineages, optimization of biotinylation conditions, and refinement of the purification process with magnetic streptavidin beads. Key features include the use of compartment-specific spatial controls to minimize nonspecific background and statistical analysis to identify true interactors. Our methodology has been validated with nuclear and cytoplasmic baits, yielding reproducible proximity interactomes. This protocol provides an efficient, reproducible, and robust framework for proximity proteomics in T. cruzi.","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"3013 ","pages":"315-342"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146106120","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

Engineering Wax Ester Composition in Euglena gracilis Using Genome Editing. 利用基因组编辑技术研究绿叶菊蜡酯的工程组成

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-5146-9_3

Sakura Nagamine, Rikuto Oishi, Masami Nakazawa

引用次数: 0

Expansion Microscopy in Euglenozoa. 真核生物的扩增显微镜。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-5146-9_13

Marie Zelená, Anežka Konupková, Vladimír Hampl, Vladimír Varga

引用次数: 0

Standardized Recombinase Polymerase Amplification (RPA) Assay for Detecting Active Trypanosoma brucei evansi Infections. 标准化重组酶聚合酶扩增（RPA）检测活动性布氏伊文氏锥虫感染。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-5146-9_9

Zeng Li, Andrés Álvarez-Rodríguez, Yann G-J Sterckx, Stefan Magez

{"title":"Standardized Recombinase Polymerase Amplification (RPA) Assay for Detecting Active Trypanosoma brucei evansi Infections.","authors":"Zeng Li, Andrés Álvarez-Rodríguez, Yann G-J Sterckx, Stefan Magez","doi":"10.1007/978-1-0716-5146-9_9","DOIUrl":"10.1007/978-1-0716-5146-9_9","url":null,"abstract":"The causative agent of \"Surra\", Trypanosoma brucei evansi (T. b. evansi), is thought to have originated from Trypanosoma brucei brucei (T. b. brucei) and primarily causes trypanosomosis in a wide range of wild and domesticated animals. The disease inflicts significant economic damage to farmers and the livestock industry. Additionally, T. b. evansi is considered a potential zoonotic pathogen, as atypical human infections have been reported. Unlike T. brucei, which requires the tsetse fly as a biological vector, T. b. evansi can be transmitted mechanically by various biting flies, leading to a broader and less predictable global distribution. The economic impact and the global presence of T. b. evansi increase the need for rapid, accurate, and field-deployable diagnostic tests. While polymerase chain reaction (PCR)-based tests are widely used for direct pathogen detection, they generally require skilled personnel and a laboratory environment to ensure proper protocol execution. In contrast, recombinase polymerase amplification (RPA) offers an alternative approach using isothermal nucleic acid amplification that is simple, fast, cost-effective, and well-suited for use in minimally equipped laboratories (and even in field settings). The results of RPA can be visualized using different methods, such as agarose gel electrophoresis (RPA-AGE), lateral flow assay (RPA-LFA), and real-time fluorescence (RPA-RT). In this chapter, we describe the procedures that are used for specifically detecting active T. b. evansi infections. The choice of procedure to be used is determined by several key factors, including the intended application, available resources, and the required sensitivity.","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"3014 ","pages":"123-135"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146106249","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

Multi-Approach Workflows for Chromatin and Histone Isolation from Trypanosoma cruzi: From Basic Protein Extraction to Mass Spectrometry-Compatible Protocols. 克氏锥虫分离染色质和组蛋白的多方法工作流程：从基本蛋白质提取到质谱兼容协议。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-5146-9_4

Ana Paula Menezes, Julia Pinheiro Chagas da Cunha

引用次数: 0

Virus-Induced Gene Silencing for Identifying Autoimmune Regulators in Arabidopsis. 病毒诱导基因沉默鉴定拟南芥自身免疫调节因子。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-5138-4_12

Suji Ye, Sung-Il Kim, Ping He

{"title":"Virus-Induced Gene Silencing for Identifying Autoimmune Regulators in Arabidopsis.","authors":"Suji Ye, Sung-Il Kim, Ping He","doi":"10.1007/978-1-0716-5138-4_12","DOIUrl":"10.1007/978-1-0716-5138-4_12","url":null,"abstract":"Virus-induced gene silencing (VIGS) has been applied as a functional genomics tool across diverse plant species. Integrated with the Arabidopsis sequence-tagged T-DNA homozygous mutant library, VIGS enables an efficient screening approach that combines features of both forward and reverse genetics, facilitating the identification of novel regulators in plant immunity. Plant defense against pathogens relies on a two-layered immune system, classified as pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). Dysregulation of key PTI or ETI components can lead to excessive or uncontrolled cell death. The cell death phenotype offers a unique avenue for genetic screens aimed at identifying suppressors of immune-related cell death. However, conventional genetic approaches face limitations due to seedling lethality and the consequent lack of viable seeds, restricting their efficiency. Here, we describe an Agrobacterium-mediated transient VIGS assay optimized for systematic gene silencing at seedling stages, leading to cell death phenotypes. This method enables high-throughput screening for cell death suppressors using T-DNA homozygous mutant collections. The platform provides a rapid, cost-efficient strategy for uncovering key regulators of plant immune signaling, offering new insights into mechanisms governing immune homeostasis and cell death suppression.","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"3012 ","pages":"165-180"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146125528","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

Plant Biotic Stress: Tools and Techniques for Crop Protection. 植物生物胁迫：作物保护的工具和技术。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-4746-2_1

Krishna Ramakrishnan Acharya, Aswin Reddy Chilakala, Muthappa Senthil-Kumar

{"title":"Plant Biotic Stress: Tools and Techniques for Crop Protection.","authors":"Krishna Ramakrishnan Acharya, Aswin Reddy Chilakala, Muthappa Senthil-Kumar","doi":"10.1007/978-1-0716-4746-2_1","DOIUrl":"10.1007/978-1-0716-4746-2_1","url":null,"abstract":"As climate change continues to impact crop yields, developing strategies to enhance plant tolerance to biotic stress has become increasingly important. This requires a thorough evaluation of the tools and methodologies used to manipulate and study biotic stress tolerance. It is crucial to comprehensively understand both conventional and modern techniques, as well as their effectiveness in addressing the specific needs of the crop under study. Detecting diseases at the early stages of plant development can prevent significant losses in large-scale cultivations. Two broad approaches commonly used to mitigate biotic stresses are eliminating causative agents such as fungi, bacteria, nematodes, viruses, or pests, and imparting resistance to the plant. Although there are similarities in the tools and techniques used to address different biotic stresses, each scenario requires dedicated case studies. It is also essential to stay up to date with the latest developments in plant biotechnology to incorporate a cross-disciplinary approach in conducting and validating experiments. This chapter provides an overview of methods covered in this book ranging from molecular breeding to nondestructive techniques that help achieve the goal of safeguarding plant health.","PeriodicalId":18490,"journal":{"name":"Methods in molecular biology","volume":"2966 ","pages":"1-20"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145200187","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

Spectroscopic Analyses of Photoconversion in Phytochromes. 光敏色素中光转化的光谱分析。

Methods in molecular biology Pub Date : 2026-01-01 DOI: 10.1007/978-1-0716-4791-2_11

Chengwei Yi, Stefanie S M Meier, Maria Kehr, Andreas Möglich

引用次数: 0