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This volume provides practical guidance on a variety of techniques and steps to ensure successful variant calling. Chapters detail methods for variant calling from single-nucleotide variants to structural variants, variant calling in specialized data types such as RNA-seq and UMI-tagged sequencing, alignment-free genotyping and SNP calling, variant detection in single-cell DNA sequencing data, variant annotation, and preanalytical quality control to ensure successful variant calling. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists step-by-step protocol to execute the algorithms, describes the input and output data, and includes tips on troubleshooting and known pitfalls. Authoritative and cutting-edge, Variant Calling: Methods and Protocols aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.  

This detailed book delves into the diverse techniques and applications to target, isolate, image, phenotype, and analyze tissue-resident and monocyte-derived macrophages. The contents aim to describe the current knowledge about macrophage development and function which forces the scientific field to move beyond the previously described M1/M2 macrophage paradigm to be able to dissect macrophage functions within their specific niches during health and disease. 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. Thorough and practical, Tissue-Resident Macrophages: Methods and Protocols provides scientists entering the macrophage field with information and tools that allow them to dive into the state-of-the-art methodology used in this vital field.

This volume details cutting-edge methods and protocols for the development, characterization, and applications of multienzyme assemblies. Chapters guide readers through up-to-date techniques applied for the development and emerging applications of multi-enzymatic systems for biotransformations, biosensing, molecular-scale diagnostics and bioelectronics. 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, Multienzymatic Assemblies: Methods and Protocols aims to be useful for academics and industry professionals working in the field of biotechnology, biochemistry, chemical and biological engineering, nanobiotechnology, and biocatalysis.

This volume covers the latest experimental protocols used by researchers to study the recently emerged fungal pathogen of humans, Candida auris, and also explores the pathogen's antifungal resistance, virulence, and pathogenicity. The chapters in this book cover topics such as the identification of C. auris in clinic samples by PCR and mass spectrometry; molecular typing to identify clade affiliation; genetic manipulation; genome analysis by bioinformatics; and phenotypic characterization using various biochemical, mass spectrometry, microscopy, and flow cytometry approaches. 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 practical, Candida auris: Methods and Protocols is a valuable resource for researchers interested in learning more about this developing field.

This volume discusses the latest approaches used to investigate molecular biology and physiology in the peripheral and central olfactory system. Understanding both normal function and pathobiology provides readers with insight into understanding human olfactory disorders. The chapters in this book cover topics such as techniques for manipulating and measuring olfactory cilia function; approaches for investigating spatial RNA expression in olfactory mucosa; the use of chromatin immunoprecipitation with olfactory neurons; in vivo methods to label and identify activated olfactory neurons; defining organization in the olfactory bulbs and cortex; and the use of optical recording in the mouse olfactory bulb for acute or chronic experiments. 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.Thorough and cutting-edge, The Olfactory System: Methods and Protocols is a valuable resource for all researchers who are interested in learning more about this important and developing field.

This volume focuses on the latest research methods and techniques used by researchers to study vascular permeability/hyperpermeability in a science laboratory setting. The chapters in this book cover topics such as determination of solute permeability of microvascular endothelial cell monolayers in vitro; evaluation of barrier integrity used in a two-layered microfluidic device mimicking the blood-brain barrier; isolation and culture of human umbilical vein endothelial cells; measurement of blood-brain barrier hyperpermeability using Evans Blue extravasation assay; lymphatic vascular permeability determined from direct measurements of solute flux; intravital imaging of leukocyte-endothelial interaction by intravital multiphoton microscopy; and evaluation of tight junction integrity in brain endothelial cells using confocal microscopy. 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.Thorough and cutting-edge, Vascular Hyperpermeability: Methods and Protocols is a valuable resource that will aid novice researchers with creating new and affordable research projects, and for expert researchers to initiate new strategies and collaborations in their ongoing programs.

This volume details well-established protocols and procedures being used by laboratories and the industry to study Predictive Microbiology in Foods. Chapters guide readers through methods to design and collect data to generate predictive models, the development of a predictive model, approaches the behavior mainly, and experiments in predictive microbiology. Written in the format of the Methods and Protocols in Food Science series, chapters list necessary materials and methods for readily reproducible protocols. Authoritative and cutting-edge, Predictive Food Microbiology aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.

This volume details generation of gene-edited cell lines and organisms as models for human diseases, pest control, and large animal welfare and production outcomes. Chapters guide readers through gene regulation, editing, screening of cell lines, genome editing, and an overview of the tools for efficient genome editing including; ZFNs, TALENs, and CRISPR. 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, Applications of Genome Modulation and Editing aims to be a useful and practical guide for researchers to commence or advance their study in this field.

This volume details step-by-step instructions on biomedical literature mining protocols. Chapters guide readers through various topics such as, disease comorbidity, literature-based discovery, protocols to combine literature mining, machine learning for predicting biomedical discoveries, and uncovering unknown public knowledge by combining two pieces of information from different sets of PubMed articles. Additional chapters discuss the importance of data science to understand outbreaks such as COVID-19.   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, Biomedical Text Mining aims to be a useful practical guide to researches to help further their studies.          

This detailed volume features techniques to explore the complex interface that separates the systemic circulation from the central nervous system, known as the blood-brain barrier (BBB). Beginning with an introduction to its physiology, the book continues with sections on using pluripotent stem cells in models of the BBB, co-culture, permeability and transwell models, microfluidic and chip models, as well as models to study specific BBB pathologies. 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, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, The Blood-Brain Barrier: Methods and Protocols collects a wide range of methodologies which will aid all researchers in the fascinating world of the blood-brain barrier.

This volume covers the detection of structural variants (SVs), which require different strategies than the ones used for single nucleotide variants (SNVs). This book aims to provide readers with a combination of the latest "wet lab" methods and computational pipelines that target all SV classes. The chapters in this book cover topics such as detection of transposable elements (TEs) from short read data; long read sequencing used for multiple variable number tandem repeat analysis; genomic mosaicism in the nervous system; and optical genome mapping. In the Neuromethods series style, chapters include the kind of detail and key advice from the specialists needed to get successful results in your laboratory. Cutting-edge and comprehensive, Genomic Structural Variants in Nervous System Disorders is a valuable resource for scientists and researchers interested in learning more about this important field.

This detailed collection explores genome-wide association studies (GWAS), which have revolutionized the investigation of complex traits over the past decade and have unveiled numerous useful genotype-phenotype associations in plants. The book describes the key concepts and methods underlying GWAS, including the genetic architecture underlying variation for phenotypic traits, the structure of genetic variation in plants, technologies for capturing genetic information, study designs, and the statistical models and bioinformatics tools used for data analysis. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of invaluable implementation advice that leads to the most fruitful research results. Authoritative and practical, Genome-Wide Association Studies serves as an extremely valuable resource for the plant research community by rendering GWAS analysis less challenging and more accessible to a broader group of users.

This detailed new edition collects cutting-edge laboratory protocols, techniques, and applications in use by some of the leading international experts in the broad field of chromosome architecture. The book emphasizes the increasing physiological relevance of chromosome architecture investigation, manifest both through application of more complex bottom-up assays in vitro as well as through maintaining the native physiological context through the investigation of living, functional cells. In addition, the chapters reflect the dramatic improvement in the length scale of precision by utilizing single-molecule approaches, both for imaging the DNA content of chromosome and proteins that bind to DNA as well as using methods that can controllably manipulate single DNA molecules, and the use of advanced computational methods and mathematical analysis is also featured. 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, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, Chromosome Architecture: Methods and Protocols, Second Edition is an ideal guide for researchers working in this dynamic area of study.

This fully updated edition introduces new tools, models, and analytic insights that position the zebrafish even more strongly as an engine of discovery for developmental and disease biology. Beginning with a section exploring detailed methods for use of zebrafish to model a variety of human diseases, the book continues by illuminating the key ongoing role of the fish model in studies of the vertebrate nervous system, tools and approaches using zebrafish to study stem cell and regenerative biology, as well as techniques in genetics and genomics. 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 up-to-date, Zebrafish: Methods and Protocols, Third Edition serves as an invaluable guide to propel advances in developmental biology, disease modeling, and regeneration research using zebrafish and medaka as model systems.

This detailed volume presents status and management protocols with the objective of identifying proper guidelines and materials for research related to the most common malignant neoplasm in the thyroid gland, papillary thyroid carcinoma. After an introduction, the book explores diagnostic approaches and initial surgical managements for patients with papillary thyroid carcinoma, guidelines for macroscopic examination, microscopic examination, and pathological staging, molecular approaches to this cancer, pathology laboratory approaches, as well as radiology oncology treatment protocols. 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 laboratory protocols that are readily reproducible, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Papillary Thyroid Carcinoma: Methods and Protocols serves as a vital resource for information on different aspects of the processes, cost, and resources available for the research and management of patients with papillary thyroid carcinoma.

This collection explores the latest advances in riboregulators, such as RNA-only systems and ribonucleoprotein systems, and provides detailed techniques to study, evolve, and design them. Beginning with a set of chapters focused on the design and application of small RNA (sRNA) regulator systems, the book continues with sections on techniques to create switchable riboregulator systems known as riboswitches, technologies that leverage RNA-guided CRISPR-Cas systems to edit the epigenome, control gene expression, and create diagnostics, as well as computational and experimental techniques to investigate the sequence-structure-function relationship of RNA systems that can both advance fundamental understanding and rational design of riboregulators. 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, readily reproducible laboratory protocols, andtips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Riboregulator Design and Analysis is an ideal guide for scientists and engineers interested in the design and application of riboregulators and driving further innovation in the field.

This volume covers various aspects of affinity chromatography along with examples of its applications. Chapters guide readers through methodologies to purify a diverse array of molecular targets such as antibodies, extracellular vesicles, recombinant proteins, biomarkers, metabolites, plant organelles, nucleic acids, ligand identification and protocols on building affinity matrix. 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, Affinity Chromatography: Methods and Protocols aims to be an invaluable resource to anyone employing affinity chromatography-based methodologies.

This volume presents current methods to detect and measure the activity of proteolytic enzymes in organisms ranging from unicellular algae to flowering plants. Chapters detail in vitro production, characterization of plant proteases, tools for in vivo modifications, proteomic approaches for identification of substrates, inhibitors and interacting partners, and the function of plant proteases in plant programmed cell death. 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, Plant Proteases: Methods and Protocols aims to be a useful practical guide to researches to help further their study in this field.

This volume provides a compilation of methods that will aid researchers studying virology, immunology, and vaccinology of this devastating disease of swine. 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, African Swine Fever Virus: Methods and Protocols aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.