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This volume compiles a comprehensive range of methods to study key aspects of mitochondrial DNA including nucleoid structure and packaging, replication, genome integrity, and disease. Chapters are organized into eight methodological sections that cover in vitro and in vivo methods, including for mtDNA isolation, visualization, deep sequencing, gene editing, and diagnostic aspects of mtDNA disease. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.Authoritative and cutting-edge, Mitochondrial DNA: Methods and Protocols aims to be useful and informative for researchers and clinicians with an interest in mitochondrial DNA.

This detailed volume provides a comprehensive resource covering the existing and state-of-the-art tools in the field of profiling chromatin accessibility and its dynamics. Beginning with a section on bulk-cell methods for profiling chromatin accessibility and nucleosome positioning that rely on enzymatic cleavage of accessible DNA and produce information about relative accessibility, the book continues with methods that use single-molecule and enzymatic approaches to solving the problem of mapping absolute occupancy/accessibility, emerging tools for mapping DNA accessibility and nucleosome positioning in single cells, imaging-based methods for visualizing accessible chromatin in its nuclear context, as well as computational methods for the processing and analysis of chromatin accessibility datasets. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, Chromatin Accessibility: Methods and Protocols serves as an extensive and useful reference for researchers studying different facets of chromatin accessibility in a wide variety of biological contexts. Chapter 6 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This volume focuses upon pollen cryopreservation in various crops from the most widely cultivated tomato to the lesser known medicinal species like Decalepis arayalpatra. Chapters detail standard techniques such as pollen collection, cryopreservation, pollen , germination tests for viability, and specific crops. Step-by-step protocols are complemented by personal notes, precautions, and specifying the reagents to be used in each step to ensure the repeatability of the procedure across labs. Authoritative and cutting-edge, Pollen Cryopreservation Protocols aims to serve as reference for researchers studying plant breeding and plant conservation biology.

This volume provides an understanding of how an immunoassay works, detailing the strengths, weaknesses, pitfalls. Chapters guide readers on how and when to appropriately utilize this powerful tool, examples of where the ELISA or similar immunoassay formats are currently being used, and newer techniques that may have a significant impact on future applications. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, ELISA: Methods and Protocols is a valuable resource for both novice and expert scientists in this developing field.

This detailed volume presents cutting-edge research protocols to study the structure and dynamics of bacterial and archaeal motility systems using bacterial genetics, molecular biology, biochemistry, biophysics, structural biology, cell biology, microscopy imaging, and molecular dynamics simulation. Beginning with a section on bacterial flagellar protein export and assembly, the book continues with chapters covering flagella-driven motility of bacteria, archaella-driven motility of archaea, type IV-driven twitching motility of bacteria, as well as adhesion-based gliding motility of bacteria and other unique motility systems. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and thorough, Bacterial and Archaeal Motility is the ideal reference for researchers working in this vital area of microbiology.

This volume details technologies on recombinant DNA and nucleic acid manipulation that underpin much of the biological sciences and instructions on how to conduct them successfully. Chapters guide the reader through the basics of oligonucleotide synthesis and DNA sequencing; recombinant DNA plasmid work; cell-free experiments and the latest developments in CRISPR approaches to genome modification. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.   Authoritative and cutting-edge, DNA Manipulation and Analysis aims to be the comprehensive guide for life scientists moving into the field of recombinant DNA and nucleic acid manipulation.

This volume provides comprehensive dry and wet experiments, methods, and applications on nanopore sequencing. Chapters guide readers through bioinformatic procedures, genome sequencing, analysis of repetitive regions, structural variations, rapid and on-site microbial identification, epidemiology, and transcriptome analysis. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Nanopore Sequencing: Methods and Protocols aims to be comprehensive guide for researchers.

This third volume provides comprehensive protocols on pre-analytical, analytical, plasma, and serum proteomics. New and updated chapters are divided into nine sections, detailing blood processing and handling strategies, discovery- and targeted-based mass spectrometry, including workflows to aid in discovery and targeted data analysis, in addition to software and bioinformatics for the plasma proteome. This edition further integrates emerging areas in the development of technologies for plasma proteomics and assay platforms in biomarker discovery and translational proteomics, enrichment and detection strategies to understand the plasma proteome, and peptide, lipid and metabolite targeted assays. We also detail the emerging analysis of extracellular vesicles isolated from plasma. Written in the format of the highly successful Methods in Molecular Biology series, each of the 33 chapters includes an introduction to the topic, lists necessary materials and methods, includes hints and tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Serum/Plasma Proteomics: Methods and Protocols, Third Edition aims to be comprehensive guide for researchers.

This thorough volume presents a wide range of existing methods, from the very popular to the more exotic, in the area of plant genotyping. Many methods of plant genotyping were initially developed for medical research, but all genotyping methods, if they are to be successful, should be suitable for application across the full range of studies within plant biology, as seen in this collection. Plant genotyping methods herein are based on a variety of assessments, including DNA microarray, with its hundreds of thousands of simultaneous reactions, or separate individual studies of DNA sequencing and fragment analysis, PCR and qPCR, allele-specific molecular probes and primers, digestion with restriction endonucleases, microscopy and many others. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Plant Genotyping: Methods and Protocols offers researchers the opportunity to update their knowledge and choose the most suitable method of plant genotyping for their chosen application.

This third edition provides new and updated chapters detailing preparation of liposomes, physicochemical characterization of liposomes, lipid analysis, drug encapsulation, surface modification, stimuli response as well as cellular interaction, and biodistribution. Also included is an updated chapter on the history and evolution of the field of liposomology. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Liposomes: Methods and Protocols, Third Edition aims to serve as a reference for graduate students, post-doctoral researchers as well as established investigators utilizing lipid-based systems.

This detailed volume explores the development of technologies and protocols that are currently being used to understand the nature and activities of the plant cytoskeleton. A focus for many of the chapters is on sample preparation, as the quality of plant organ/tissue preparation, from single to multicellular samples, determines the quality of the data. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, The Plant Cytoskeleton: Methods and Protocols serves as an ideal guide for researchers interested in or starting to be interested in plant cell and molecular biology research.

This second edition provides new and updated protocols that can be used for generation of knockout animals. Chapters guide the reader through basic protocols for three genome editing technologies, target design tools, and specific protocols for each animal. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Genome Editing in Animals: Methods and Protocols, Second Edition aims to be a useful practical guide to researches to help further their study in this field.

This volume provides protocols on evidence for polyploidy and how it can be unveiled. Chapters guide readers through evolutionary experiments, measure effects of polyploidy, evidence for (remnants of) ancient WGDs, models of chromosome number evolution, population genomics approaches to study polyploidy, analysing genetic data from polyploid populations, Phylogenetic and phylogenomic methods, gene expression, gene regulation, unicellular alga (Chlamydomonas),  and a fast-growing duckweed (Spirodela). Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Polyploidy: Method and Protocols aims to be of interest to experimental and computational (evolutionary) biologists, molecular biologists, and biotechnologists.

This volume details state-of-the-art computational methods designed to manage, analyze, and generally leverage epigenomic and epitranscriptomic data. Chapters guide readers through fine-mapping and quantification of modifications, visual analytics, imputation methods, supervised analysis, and integrative approaches for single-cell data. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Computational Epigenomics and Epitranscriptomics aims to provide an overview of epiomic protocols, making it easier for researchers to extract impactful biological insight from their data.

This book explores recent progress in RNA secondary, tertiary structure prediction, and its application from an expansive point of view. Because of advancements in experimental protocols and devices, the integration of new types of data as well as new analysis techniques is necessary, and this volume discusses additional topics that are closely related to RNA structure prediction, such as the detection of structure-disrupting mutations, high-throughput structure analysis, and 3D structure design. Written for the highly successful Methods in Molecular Biology series, chapters feature the kind of detailed implementation advice that leads to quality research results. Authoritative and practical, RNA Structure Prediction serves as a valuable guide for both experimental and computational RNA researchers.

This detailed volume compiles numerous methods to explore fly oogenesis. Beginning with updated protocols from isolating and staining the ovary to numerous imaging techniques and genetic protocols for cell-specific assessment and CRISPR-mediated mutagenesis, the volume continues by detailing techniques from assessing cytoskeletal structures to uncovering protein-protein interactions, with closing chapters exploring how Drosophila oogenesis can be used in the classroom and in outreach programs to increase interest in biomedical research, STEM education, and STEM careers. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Drosophila Oogenesis: Methods and Protocols serves as an ideal guide for both new and expert researchers working with this robust and versatile model organism.

This detailed collection explores a diverse range of topics related to neural repair and functional recovery following ischemic stroke. Techniques detailed in this book span from basic to emerging approaches used to evaluate hallmarks of neurorepair, including axonal remodeling and dendritic arborization, plasticity and functional connectivity, angiogenesis, neuroinflammation, and recovering cerebral blood flow. In addition, several chapters focus on rodent stroke models and post-stroke functional evaluation, clinically-relevant therapeutic paradigms and co-morbidities, pharmacotherapy and methods of delivery. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, as well as tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Neural Repair: Methods and Protocols serves as an ideal guide for the wide community of researchers interested in neurorepair following stroke and other forms of CNS injury.

This volume combines well-established state-of-the-art techniques and innovative technologies in the field of emotions and applying them to food and sensory sciences. Chapter guide readers through explicit measures of emotions, protocols enabling the measure of implicit aspects of emotions, and protocols enabling analysis of complex and voluminous data generated by emotion studies in food science. Authoritative and cutting-edge, Basic Protocols on Emotions, Senses, and Foods aims to provide researchers the most complete information possible in terms of stimuli, materials, and methods for characterizing emotions, in order to give them the possibility of taking on new projects and new challenges in food science.

This updated volume reflects new and evolved techniques to study detection, profiling, and manipulation of microRNAs (miRNAs) in plants and animals. After overviews of how best to detect, identify, and validate microRNAs, the book continues by exploring state-of-the-art protocols for microRNA detection, approaches to profile the expression level of microRNAs, spatial expression analysis, describe in silico analysis of microRNAs and their targets, as well as protocols for functional analysis of microRNAs and their targets by CRISPR/Cas. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, MicroRNA Detection and Target Identification: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

This volume is a comprehensive and up-to-date collection of strategies, reproducible methods, and protocols for the in-depth analysis of Proteoglycans (PGs) and their glycan part, the GAGs. Chapters are divided into three parts detailing GAGs in biological specimens, protocols for the evaluation of the in vitro and in vivo effects of PGs/GAGs, and protocols for compounds related with the metabolic enzymes, epigenetic regulation, and PGs/GAGs-based inhibitors. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.Cutting-edge and thorough, Proteoglycans: Methods and Protocols aims to provide information on the elucidated the structural and functional aspects of the complex matrix macromolecules such as the proteoglycans and glycosaminoglycans.

This detailed volume presents a series of protocols dealing with different aspects of inclusion body (IB) processing, from cloning procedures to purification of refolded product. Commencing with chapters on upstream processing, looking into different expression strategies for IB production, the book continues with downstream applications, highlighting early protein purification and subsequent analytics, as well as success stories of IB-based processes. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Inclusion Bodies: Methods and Protocols serves as an ideal resource for facilitating diverse aspects of IB processing.

This fully updated book presents an account of areas of utility, techniques, and bioinformatic advancements in the field of lipidomics. Beginning with protocols for lipid isolation and extraction, the volume continues with techniques from extractive mass spectrometry to imaging mass spectrometry methods allowing localization of lipids in tissues. These protocols have been complemented by methods addressing specific problems from membranes, fractionated subcellular compartments or organelles to whole organisms. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, as well as tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Lipidomics: Methods and Protocols, Second Edition serves as an ideal guide for biochemists, molecular biologists, neuroscientists, vision research scientists, as well as all biomedical researchers with interest in disease discovery and drug development.

This detailed collection serves as a unique and excellent collection of state-of-the-art methods and protocols to interrogate cell migration in a wide variety of different contexts and model organisms, as well as advanced image analysis and quantitative assessment of a diverse array of parameters related to cell migration. The book focuses on the cell biology of cell migration, developmental model systems to assess cell migration during morphogenesis, cell migration in cancers and the tumor micro-environment, as well as blood vessel formation and interactions. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Cell Migration in Three Dimensions provides a solid foundation for scientists of different disciplines to investigate cell migration in biological processes. Chapters 7, 12, 16, 17, 19, 22, and 24 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This volume provides a collection of protocols from leading researchers in the dynein field. The enclosed chapters guide readers through a broad range of powerful techniques that can be used to understand the complexities of dynein activity and regulation. These include how to perform live-cell microscopy on various fungi and metazoan cells, how to purify, assemble, and measure the force generation and motility characteristics of various dynein assemblies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Dynein: Methods and Protocols is a valuable resource for both novice and expert scientists in this developing field.