Books in the Methods in Molecular Biology series

This volumes details methods focusing on technological innovation and recent advances in diabetes management. Chapters will guide readers through recent advances, beta-cell regeneration, non-invasive imaging of endogenous, transplanted islets theranostics, microRNA profiling of beta-cells and artificial intelligence, and deep learning algorithms in diabetes. 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, Type-1 Diabetes: Methods and Protocols is for a broad audience including basic researches, clinicians, and physician scientists whose major focus is in diabetes.

This volume provides up-to-date methods on single cell wet and bioinformatics protocols based on the researcher experiment requirements. Chapters detail basic analytical procedures, single-cell data QC, dimensionality reduction, clustering, cluster-specific features selection, RNA velocity, multi-modal data integration, and single cell RNA editing. 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 comprehensive, Single Cell Transcriptomics: Methods and Protocols aims to be a valuable resource for all researchers interested in learning more about this important and developing field.

This second edition provides state-of-the-art and novel methods on antibiotic isolation and purification, identification of antimicrobial killing mechanisms, as well as methods for the analysis and detection of microbial responses and adaptation strategies. Antibiotics: Methods and Protocols,  Second Edition, guides readers through updated and entirely new chapters on production and design, mode of action, and response and resistance. 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. Authoritative and cutting-edge, Antibiotics: Methods and Protocols, Second Edition aims to inspire scientific work in the exciting field of antibiotic research.

This second edition provides new and updated methods detailing techniques and state-of-the-art approaches on the structure and function of plant endoplasmic reticulum (ER). Chapters guide readers through modern microscopy techniques, software protocols, purification, and analysis of ER membrane structure. 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, The Plant Endoplasmic Reticulum: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

This second edition provides updated and comprehensive methods on miRNA biogenesis and their role in the development and progression of various human diseases. Chapters detail miRNA biogenesis, isolating RNA, extracellular vesicles (EVs), circulating miRNAs, analyzing miRNA and miRDeep-P2, protocols for total RNA isolation from cells, cell-derived products, isolation and characterization of exosomes, serum, plasma specimens, and software tools. 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, MicroRNA Profiling: Methods and Protocols, Second Edition aims to provide comprehensive and accessible methods to undergraduate, graduate, and established scientist.

This volume details protocols emphasizing systems-level approaches that can be applied to genomic analyses. Chapters detail techniques for optimized application in in vivo systems, spatial, physiological, environmental contexts, imaging-based techniques, single-molecule approaches, CRISPR systems, new genomic approaches, and measurements of kinetics governing. 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, DNA-Protein Interactions: Methods and Protocols aims to present genome-wide techniques that will complement the biochemistry-based protocols to aid researchers in their studies. 

This second edition details new and updated methods on circular RNA. Chapter guide readers through circular RNA purification, in silico characterization, circRNA detection, sequence validation, quantification , techniques related to gain- and loss-of-function approaches, circular RNA synthesis, split ligation, engineering, nanoparticle packaging, RNA modifications on circular RNA biogenesis, RNA translation potential, and vaccines based on circular RNAs. 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, Circular RNAs, Second Edition aims to ensure successful results in the further study of this vital field.

This volume discusses the latest advancements in modern methodologies used to study liver carcinogenesis. The first half of this book describes pertinent preclinical models of hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), established either through orthotopic induction of ectopic implantation. The second half of this book covers a diverse array of techniques applied to characterize the biochemical and cellular composition of hepatic malignancies that operate at the single-cell and histological levels. 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 comprehensive, Liver Carcinogenesis: Methods and Protocols, is a valuable resource for students and scientists who are interested in drivingprogress in the important field of liver cancer research.

This second edition explores standard laboratory protocols and methodology commonly used in basic and translational studies in the field of rheumatoid arthritis (RA) treatment. Chapters detail including basic RA models, evaluation of disease activity and immunological status, systemic drug delivery, and new research tools. 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, Rheumatoid Arthritis: Methods and Protocols, Second Edition aims to be a basic manual for clinical researchers who are just getting started in the field of intervention study.

 This volume details the history of Retinitis Pigmentosa and current treatment options. Chapters guide readers through CRISPR, gene therapy, stem cell therapy, next-generation sequencing methods, gene editing, and translational applications of other therapies to the treatment of Retinitis Pigmentosa. 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, Retinitis Pigmentosa aims to be a useful practical guide to researches to help further their study in this field.  

This detailed volume explores techniques for the isolation, purification, and establishment of in vitro germ cell (GS) systems at different stages of development in a variety of organisms, including chickens, mice, rats, and humans. The book additionally describes cutting-edge analytic and informatic tools to study germ cell development at the single cell level and meiotic recombination. 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 and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Germ Cell Development: Methods and Protocols provides new insight into the understanding of basic biological aspects of germ cell biology, as well as the opportunity for in vitro manipulation of germ cells for toxicology studies and for genetic intervention.

Since the publication of the previous edition, the use of 3D cell and organoid cultures has become more widespread across laboratories. This second edition volume expands on the previous edition with discussions about the latest organoid models developed for many more organs; new hydrogels and devices for 3D culture; and the organoid systems that have been improved by incorporating more components of tissue microenvironments in the in vitro culture. The chapters in this book are organized into five parts and cover topics such as biofabrication, organoids, microfluidic systems, bioprinting, and image analysis. 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, 3D Cell Culture: Methods and Protocols, Second Edition is a valuable resource that will stimulate new ideas, foster interdisciplinary collaborations, and contribute to the improvement of human health and well-being.

This volume explores the latest techniques used to study the human brain towards understanding Alzheimer¿s Disease and related neurodegenerative disorders. Contributed to by world-renowned experts, the chapters in this book are divided into five parts. Part One discusses human post-mortem brain preparations including single-cell isolation and use of specialized imaging. Part Two talks about neural cellular models using primary and human induced pluripotent stem cells to model aspects of the human brain. Part Three details nucleic acid analyses including transcriptomic and somatic genomic changes, and Part Four discusses lipid analyses via mass spectrometry. Lastly, Part Five covers protein analyses, particularly Aß and Tau. 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, Alzheimer¿s Disease: Methods and Protocols is a valuable tool for all researchers who want to expand their knowledge and understanding of this disease and other related dementias.

This detailed volume provides methods to guide assay development, procedures designed to investigate the chemokine and glycosaminoglycan (GAG) networks, as well as their interactions, in a wide range of organs and tissues in disease and in health. The initial chapters in this book present in vivo models used to examine the roles of chemokines and GAGs in normal physiology and in the pathophysiology of disease. The book then explores present cell- and tissue-based in vitro assays to examine chemokine:GAG interactions. Finally, analytic approaches are presented that provide assays for measuring GAGs, chemokines, and cellular responses. 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, Chemokine-Glycosaminoglycan Interactions: Methods and Protocols serves as an ideal guide for researchers seeking to analyze chemokine and GAG functions, interactions, and molecular mechanisms in vivo and in vitro.

The second edition of this volume provides a comprehensive update of this key method on gel-based proteomics. Chapters present an introduction into the development of methods on principles of differential protein labeling and two-dimensional gel electrophoresis, techniques on optimized proteomic workflows using advanced mass spectrometry for protein identification, and the application of those methods in basic biological research, pathobiology and applied biomarker discovery. 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. Authoritative and cutting-edge, Difference Gel Electrophoresis: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field. 

This second edition volume expands on the previous edition with updated methodologies and practical tips to overcome obstacles associated with experimentation pertaining to chemistry, biology, physiology, pathology, medical and dental sciences, and pharmacology of CCN proteins. The chapters in this book cover topics such as CCN4 immunofluorescence for tissue microarray; utilizing public molecular biological databases for CCN family research; the effects of CCN4 on pancreatic beta cell proliferation; gene expression analysis of CCNs; novel cell biological assays for measuring bone remodeling activities of CCN proteins; and the function of CCN2 in tubular epithelium cells with a focus on renal fibrogenesis. 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 comprehensive, CCN Proteins: Methods and Protocols, Second Edition is a valuable resource for experienced CCN researchers looking for new approaches and novice researchers just starting out in the field of CCN research.

This detailed book presents a comprehensive collection of state-of-the-art protocols on muscular dystrophy therapeutics, covering therapeutics using antisense oligonucleotides, gene replacement, genome editing, small molecules, stem cells, and antibodies. Written by leaders in the field, the volume explores techniques that are currently in use and are starting an exciting therapeutic revolution in muscular dystrophy. As a part of 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, Muscular Dystrophy Therapeutics: Methods and Protocols serves as an ideal resource to inspire readers and provide tips, strategies, and advice to develop new therapeutic technologies for this group of diseases.

This second edition volume provides new and updated chapters detailing simple and accessible experiment protocols to explore thymus biology. Chapters are divided into three parts presenting short reviews, analysis strategies, protocols for cell preparation, flow cytometry analyses, Innate Lymphoid Cells (ILC), mouse T-cell development, antigen receptor-less cousins of T cells, bone marrow chimeras, thymic stroma, and multiple aspects of thymocyte biology. 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, T-Cell Development: Methods and Protocols, Second Edition aims to be a useful practical guide to help readers overcome obstacles associated with experimental approaches of T-cell development.

The volume details techniques, methods, and conceptual developments to further the study of protein aggregation with emphasis on the pleiomorphic proteins implicated in etiology of neurodegeneration. Chapters guide readers through in vitro and in vivo studies of fibrillization and liquid-liquid phase separation processes, and offer a comprehensive account of the state-of-art of structural studies of protein aggregation. 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, Protein Aggregation: Methods and Protocols aims to be useful and practical guide to new researchers and experts looking to expand their knowledge.

This volume contains cutting-edge molecular biology methods on neuroprotective mechanisms and specific preclinical models of the CNS injury, iseases and planning translation. Chapters guide readers through neuropathology, neuroprotection, Alzheimer¿s disease, amyotrophic lateral sclerosis, ALS, Huntington¿s disease , multiple sclerosis, Parkinson¿s disease, spinal cord injury, traumatic brain injury, and ischemic brain injury. 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. Authoritative and cutting-edge, Neuroprotection: Methods and Protocols aims to ensure successful results in the further study of this vital field.

This second edition provides new and updated techniques and applications associated with synthetic biology. Chapters guide readers through the creation and regulation of gene circuits, manipulation of biochemical pathways, genome editing and modification, creating genome language and computing, as well as molecular assembly.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, Synthetic Biology: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

This volume explores the latest advancements and techniques used by researchers to work with plant parasitic nematodes (PPNs) and to study their interactions with crop plants. The chapters in this book cover topics such as ways to obtain samples from soil and different plant tissues; rearing nematodes in greenhouse setting; methods used to axenically rear nematodes in vitro; Denaturing Gradient Gel Electrophoresis (DGGE) separation; methods for ROS detection and hydrogen peroxide quantification; methods to elicit plant resistance against nematodes; methods for the detection of Pathogenesis Related (PR) genes that are the executioners of immunity in plant-RKN interactions; and laboratory procedures that test nematodes on their isolation, count, culture, identification, pathogenicity, virulence, and environmental tolerance. 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, Plant-Nematode Interactions is a valuable tool for any researcher interested in learning more about this interesting and developing field.

This book aims to be an introduction to haplotype information for both the wet and dry labs. Chapters detail co-barcoding and linked-reads based methods, third generation sequencing based methods, Hi-C based methods, single-cell and Strand-seq, and methods for using haplotype data once obtained. 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, Haplotyping: Methods and Protocols aims to provide comprhensive and accessible methods to undergraduate, graduate, and established scientists.

This book aims to advance the understanding of deubiquitinases (DUBs) and DUB-like enzymes. Chapters detail methods used to identify, classify,and biochemically characterize DUBs along with approaches that enable both the determination and alteration of DUB biological function.. 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, Deubiquitinases: Methods and Protocols aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge. 

This volume details state-of-the- art methods on computer-aided antibody design. Chapters guide readers through information on antibody sequences and structures,  modeling antibody structures and dynamics, prediction and optimization of biological and biophysical properties of antibodies, prediction of antibody-antigen interactions, and computer-aided antibody affinity maturation and beyond. 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, Computer-Aided Antibody Design aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge. Chapter 2 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This volume provides a comprehensive reference for researchers aiming to bring new techniques and approaches to their scientific research using urodeles. Chapters are authored by leaders in the field and meant to guide readers through laboratory colony husbandry, traditional molecular techniques, experimental manipulation and surgeries, bioinformatics and genomics, transgenics and lineage-tracing, and physiological and organismal techniques. In addition to laboratory methods, this volume highlights techniques developed for field studies and work with wild-caught animals. 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 state-of-the-art, Methods in Salamander Research aims to be a practical guide for researchers interested in deploying new  methodologies in their lab or in the field. 

This volume provides researchers with the most updated understanding of the basics of West Nile Virus (WNV). Chapters focus on the biology, virology, epidemiology, pathogenesis, as well as the step-by-step molecular, cellular, and statistical methods to study WNV infection in cell culture, mosquitos, animal models, and human clinical specimen.  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 comprehensive, West Nile Virus: Methods and Protocols aims to be a valuable resource for all researchers interested in learning more about this important and developing field.

This book combines discursive chapters that present the latest progress in molecular biology, drug discovery, organ-tissue engineering, and related fields, with a number of descriptive chapters on methods, protocols, and case studies. Structured into four parts, this volume walks the reader through the latest in cellular biology, with discussions on novel medicinal plant metabolites, nanotechnology in precision medicine, nucleic acid-based therapeutics and vaccines, genetic engineering, computational aid, bioinformatics, synthetic organs for transplantation, and organ-tissue engineering. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that ensures quality results in the lab. Authoritative and informative, Gene, Drug, and Tissue Engineering serves as an ideal guide for undergraduate students, postgraduate researchers, and senior researchers working in biomedicine and its underlying technologies, stimulating both computational and experimental development and fostering the exchange of new ideas.

This book explores the most important processing steps of proteomics data analysis and presents practical guidelines, as well as software tools, that are both user-friendly and state-of-the-art in chemo- and biostatistics. Beginning with methods to control the false discovery rate (FDR), the volume continues with chapters devoted to software suites for constructing quantitation data tables, missing value related issues, differential analysis software, and more. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and implementation advice that leads to successful results. Authoritative and practical, Statistical Analysis of Proteomic Data: Methods and Tools serves as an ideal guide for proteomics researchers looking to extract the best of their data with state-of-the art tools while also deepening their understanding of data analysis.