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This volume details features of DNA methylation data, data processing pipelines, quality control measures, data normalization, and to discussions of statistical methods for data analysis, control of confounding and batch effects, and identification of differentially methylated regions. Chapters focus on microarray-based methylation measures and sequence-based measures. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary methodologies and software packages, step-by-step, readily reproducible analysis pipelines, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Epigenome- Wide Association Studies: Methods and Protocols: aims to be a useful practical guide to researches to help further their study in this field.

This third edition details new and updated methods and protocols on important databases and data mining tools. Chapters guides readers through archives of macromolecular sequences and three-dimensional structures, databases of protein-protein interactions, methods for prediction conformational disorder, mutant thermodynamic stability, aggregation, and drug response. Quality of structural data and their release, soft mechanics applications in biology, and protein flexibility are considered, too, together with pan-genome analyses, rational drug combination screening and Omics Deep Mining. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials, includes step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Data Mining Techniques for the Life Sciences, Third Edition aims to be a practical guide to researches to help further their study in this field.

This collection explores state-of-the-art methods and protocols for research on photodynamic therapy (PDT) and its use in a wide range of medical applications, from antiviral to anticancer. Beginning with an extensive section on in vitro and in vivo models, the volume continues with chapters on oxygen-independent photosensitizers, next-generation photosensitization strategies, contemporary insights into the immunomodulatory effects of PDT, antimicrobial effects of PDT, as well as a variety of general biochemical and molecular biological techniques. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that ensures successful results in the lab. Thorough and authoritative, Photodynamic Therapy: Methods and Protocols serves as an ideal source of inspiration for both new and established PDT scientists and a guide for designing innovative research programs in this continuously advancing and multidisciplinary field.

This second edition provides detailed practical information on important methods employed in the engineering of plant secondary metabolism pathways. New and updated chapters guide readers through extraction, quantification, purification, localization, characterization, data mining and processing, biosynthesis modulation, and pathway engineering of representative classes of plant specialized metabolites. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, list of necessary materials and reagents, tips on troubleshooting and known pitfalls, and step-by-step descriptions of readily reproducible protocols. Authoritative and cutting-edge, Plant Secondary Metabolism Engineering: Methods and Protocols, Second Edition aims to be a useful practical guide to help researchers working in this exciting field.

This second edition volume discusses the latest techniques and protocols used in the field that were not covered in the previous edition. The chapters in this book are organized into five parts. Part One looks at transcriptomic analyses and Part Two covers DNA replication and protein/DNA interactions. Part Three discusses translation dynamics, protein complexes, and proteomics. Part Four looks at genotypic screens and phenotypic profiling, and Part Five explores in silico integration of functional genomics data. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary material and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.Cutting edge and practical, Yeast Functional Genomics: Methods and Protocols, Second Edition is a valuable resource for all researchers interested in learning more about the evolving field of yeast.Chapters 1, 9, 16, 20, 22, 24, and 25 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This volume highlights natural products, molecular methods for identifying, and current trends in designing non-natural natural products. Chapters guide readers through protocols on heterologous expression techniques, gene disruption, modified pathway regulators, and in-vitro studies. 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, Engineering Natural Product Biosynthesis: Methods and Protocols aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge. Chapter 13 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This book aims to deliver the most up-to-date protocols in using epiblast stem cells (EpiSC) to answer critical questions on mammalian development. Beginning with a section on the spectrum of mouse primed pluripotent stem cells, the volume continues with chapters on toolkits to characterize and study primed stem cells, as well as primed stem cells to engineer gastrulation models. Written for the highly successful Method 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, Epiblast Stem Cells: Methods and Protocols serves as an ideal guide to overcome the reproducibility problem by gathering detailed state-of-the-art protocols to perform comprehensive analyses, enabling the reader to opt for the appropriate cell type to model the epiblast.

This second edition details new and updated chapters on key methodologies and breakthroughs in the mass spectrometry imaging (MSI) field. Chapters guide readers through nano-Desorption Electrospray Ionisation (nDESI), Matrix Assisted Laser Desorption Ionisation-2 (MALDI-2), Laser Ablation - Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS) ,Imaging Mass Cytometry (IMC) with a variety of diverse samples including eye tissue, crop analysis, 3D cell culture models, and counterfeit goods 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 reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Imaging Mass Spectrometry: Methods and Protocols, Second Edition aims to be a useful and practical guide to new researchersand experts looking to expand their knowledge.

This volume explores updated and entirely new experimental approaches used to investigate phagocytosis and phagosome maturation. In order to aid in the study of engulfment, maturation, resolution, and pathogen manipulation of phagocytes, the book features methodology to quantify uptake and maturation specific to certain phagocytes, particles, or pathogens, while other chapters offer methods that can be applied generically across the field. Methods are presented to study phagocytosis and phagosome maturation in vivo, in cellulo, and through in vitro analyses. 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, Phagocytosis and Phagosomes: Methods and Protocols, Second Edition serves as a vital resource for both experts in the field as well as for investigators delving into phagocytosis and phagosome maturation for the first time.

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 detailed volume provides the increasing number of SARS-CoV-2 researchers with a useful handbook covering multidisciplinary approaches on various aspects of SARS-CoV-2 research, brought together by leading laboratories across the globe. Topics covered include techniques in clinical and diagnostic virology, basic protocols in cell and virus culture, as well as bioinformatics and proteomics approaches in cellular response studies. This comprehensive collection also covers methods in immunology, animal models, antivirals and vaccine development strategies, as well as biorisk and mitigation measurements for SARS-CoV-2 research. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that is vital for success in the lab. Practical and timely, SARS-CoV-2: Methods and Protocols serves as an ideal guide for scientists investigating this prevalent and perilous RNA virus and the novel coronavirus disease that results from it.

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 explores a collection of methods that studies genome editing across a variety of bacteria, phages, and plants. Chapters in this book cover topics such as scarless DNA recombineering of phage in the lysogenic state; HEMSE; Dup-In and DIRex; recombineering in Staphylococcus aureus; and genome editing with Cas9 in lactobacilli. 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, Recombineering: Methods and Protocols is a valuable resource for any researchers interested in learning more about this developing 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.

This book analyzes liquid biopsy applications in cancer and other diseases. Chapters guide readers through the latest technologies and analysis methods for liquid biopsy,liquid biopsy in cancer, role of liquid biopsies in rheumatoid arthriti, cell-free circulating DNA profiling in patients with skin diseases, circulating non-coding RNAs, and exomes. 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, Liquid Biopsies: Methods and Protocols aims to attract more researchers and clinicians to study the diagnosis, immunotherapy, and prognosis of cancer and other diseases with liquid biopsy analysis.

This volume provides methods on the role of TLRs in immune responses and on the various approaches targeting different TLRs in cancer, autoimmunity and in vaccine development. 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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Toll-Like Receptors: Methods and Protocols aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge.

This second edition details protocols that analyze and explore gene regulatory networks (GRNs). Chapters guide readers through experimental techniques used to study genes and their regulatory interactions in plants, and computational approaches used for the integration of experimental data and bioinformatics-based predictions of regulatory interactions. 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 Gene Regulatory Networks: Methods and Protocols, Second Edition aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge.

This second volume focuses on PCR methods and PCR application specificities to the biotechnology and bioengineering field. New and updated chapters detail real-time PCR protocols, synthetic biology applications, pathogen detection, microfluidics, digital, multiplex detection recent advances. 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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, PCR: Methods and Protocols, Second Edition aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge.

This third edition volume expands on the previous editions with new discussions on the latest techniques and developments in the field. The chapters in this book are organized into four parts, and cover topics such as optical tweezers; single-molecule fluorescence tools; atomic force microscopy; magnetic tweezers; applications to virus protein shells, unfolding of proteins, nucleic acids, motor proteins, in vivo and in vitro; and protocols to establish specific surface interactions and perform force calibration. 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, Single Molecule Analysis: Methods and Protocols, Third Edition is a valuable resource for all researchers who wantto learn more about this exciting and still expanding field.Chapters 2, 7, 8, 9, 12, 18, and 19 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This second edition details new and updated methods on different antibody libraries, along with novel approaches for antibody discovery. Chapters focuses on the construction of antibody libraries, antibody expression, complementary approaches for antibody selection, and other phage display related applications. 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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Phage Display: Methods and Protocols, Second Edition aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge.

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 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 volume explores experimental laboratory procedures for a wide range of steroid bioconversions. After an overview on the current trends and perspectives, the book continues with sections covering microbial screening and synthetic biology applied to microorganisms able to catabolize sterols, methods on strain characterization, including omics and biochemical analyses, methods of fermentation and biocatalysis for steroids production, as well as a chapter on the medical use of glucocorticoids in cancer patients. 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, Microbial Steroids: Methods and Protocols, Second Edition serves as an ideal reference source for laboratory and industrial professionals, as well as for students in a wide array of biological disciplines.

This volume discusses the latest online plant genomics and cytogenetic resources used by plant evolutionary biologists and plant breeders. The chapters in this book are organized into two parts. Part One looks at plant genomic databases, and covers topics such as plant phenomics and genomics research data repositories, InpactorDB, PlanTEenrichment, and PEATmoss, among others. Part Two looks at cytogenetics and chromosome-related databases, and covers resources such as the Plant DNA C-values database, the Delphineae Chromosome Database (DCDB), B-chrom, a Database on B-chromosomes, and the Plant Ribosomal DNA Database. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective databases and offers explicit directions on how to access and get the most of these resources. Cutting-edge and comprehensive, Plant Genomic and Cytogenetic Databases is a valuable instrument for any plant science researcher who is interested in learning more about the wealth of information that is available through the use of these databases.