Books published by Springer US

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 second edition explores techniques involving pseudogenic DNA, RNA, and proteins. Chapters describe how to identify pseudogenes and how to study the functions and alterations of pseudogenic RNA and proteins, both in vitro, and in vivo. Written in the highly successful Methods in Molecular Biology series format, methodological 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 while avoiding known pitfalls.Authoritative and cutting-edge, Pseudogenes: Functions and Protocols, Second Edition aims to be a practical guide to researches, useful to help further their study in this field.

This volume presents techniques needed for the study of long non-coding RNAs (lncRNAs) in cancer from their identification to functional characterization. Chapters guide readers through identification of lncRNA expression signatures in cancer tissue or liquid biopsies by RNAseq, single Cell RNAseq, Phospho RNAseq or Nanopore Sequencing techniques; validation of lncRNA signatures by Real time PCR, digital PCR or in situ hybridization; and functional analysis by siRNA or CRISPR based methods for lncRNA silencing or overexpression. Lipid based nanoparticles for delivery of siRNAs in vivo, lncRNA-protein interactions, viral lncRNAs and circRNAs are also treated in this volume. 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 practical, Long Non-Coding RNAs in Cancer aims to provide a collection of laboratory protocols, bioinformatic pipelines, and review chapters to further research in this vital field.

1. Introduction.- 1.1. The changing interest for housing in development theory and policy.- 1.2. Appraisal of low-income housing.- 1.3. Scope and structure of the study.- 2. Malaysia.- 2.1 Location and climate.- 2.2. Historical perspective.- 2.3. Demographic trends.- 2.4. The Malaysian economy.- 2.5. The political background to development planning.- 2.6. Development planning in Malaysia.- 3. Housing in Peninsular Malaysia.- 3.1. Introduction.- 3.2. Housing as a goal: needs and supply in Peninsular Malaysia.- 3.3. Macroeconomic aspects of investment in housing.- 3.4. Squatter settlements.- 4. Evaluation of Squatter Rehousing.- 4.1. Cost-benefit analysis (CBA) of squatter rehousing.- 4.2. Methodological aspects.- 4.3. The case-study rehousing schemes.- 5. Estimation of National Parameters for Peninsular Malaysia.- 5.1. National goals and their relative importance.- 5.2. The social discount rate (SDR).- 5.3. Accounting ratios.- 5.4. Summary review of national parameters.- 6. Case-Study Analysis.- 6.1. Introduction.- 6.2. Rate of return analysis.- 6.3. Miscellaneous impacts.- 6.4. Summary results of case-study analysis.- 7. Main Conclusions.- 7.1. Summary review.- 7.2. Generalizations possibilities and suggestions for further research.- Appendix A. A survey of cost-benefit analysis.- Appendix B. Impact of squatter rehousing on selected social variables.- Appendix C. Estimates of costs and benefits for all schemes.- Appendix D. Tabulated results of sensitivity analysis.- Appendix E. Significance tests used.- References.- List of Abbreviations.- List of Symbols.

This volume focuses on protein analysis, and covers a wide array of uses of protein microarray for disease analysis. The chapters in this book discuss different stages of protein microarrays from their construction to their use, including different types of protein microarrays such as recombinant proteins, antibody, phage, and NAPPA protein microarrays, in planar format or in solution via beads arrays. 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.Comprehensive and cutting-edge, Protein Microarrays for Disease Analysis: Methods and Protocols is a valuable resource for graduate and post-doctoral fellows interested in protein microarrays, as well as senior researchers interested in gaining more insight into this developing field.

This volume in the Encyclopedia of Complexity and Systems Science, Second Edition, covers recent developments in classical areas of ergodic theory, including the asymptotic properties of measurable dynamical systems, spectral theory, entropy, ergodic theorems, joinings, isomorphism theory, recurrence, nonsingular systems. It enlightens connections of ergodic theory with symbolic dynamics, topological dynamics, smooth dynamics, combinatorics, number theory, pressure and equilibrium states, fractal geometry, chaos. In addition, the new edition includes dynamical systems of probabilistic origin, ergodic aspects of Sarnak's conjecture, translation flows on translation surfaces, complexity and classification of measurable systems, operator approach to asymptotic properties, interplay with operator algebras

This is the third volume on gastrointestinal cancer of the Cancer Treatment and Research Series. The emphasis in this volume is to present a series of papers on areas of high clinical relevance in malignant diseases of the gut. As in the first and second volumes of this series, authors have been selected for their expertise and national and international prominence in their fields. This volume is organized so that papers explaining basic science pro spec- tives proceed those dealing with clinical aspects of gastrointestinal cancer. It is clear that in many instances advances gastrointestinal carcinoma cannot be effectively treated if ' cure' is the desired goal. When faced with poorly treatable diseases it is obviously important to look toward the causes and prevention of these illnesses. For this reason, there are several chapters in this volume that examine the issue of carcinogenesis of gastrointestinal cancer. Likewise, in diseases that are poorly treatable in advances stages, one is interested in early detection. Thus, early screening of populations becomes important and is dealt with in three papers in this volume. Chapt- ers on treatment explore innovative approaches to therapy of gastrointesti- nal cancer. Second-look surgery with resection, arterial perfusion with che- motherapy, adjuvant therapy and neoadjuvant therapy are all addressed in various chapters in this volume. Finally, four chapters deal with unusual problems in gastrointestinal cancer. These papers include discussions ofpri- mary hepatobillary cancer, lymphoma of the gut, and gastrointestinal endo- crine tumors.

This volume brings together classical and cutting-edge protocols on the spatio-temporal study of the cellular subsets constituting the bone and the marrow in both mouse and human. Chapters details methods on bone marrow (BM) ecosystem, to label, sort, analyse, and culture specific cell subsets as well as techniques allowing the evaluation of the function of some of the cellular elements of the BM. 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, Bone Marrow Environment: Methods and Protocols aims to help new investigators to pursue the characterization of the BM microenvironment in the coming years.

This new edition explores lab protocols describing new techniques to study cytotoxic T-cells (CTLs), as well as chapters of a more general discursive nature, all with an emphasis on the use of systems biology in immunology. Beginning with phenotypical characterization of CTL populations, the volume continues with in vitro and in vivo cytotoxicity assays, methods to detect senescent T cells, in vivo and in vitro models to understand immune and bone cells cross-talk, microscopy and in vivo imaging, as well as ¿Omics¿ approaches and molecular methods, concluding with chapters on CTL involvement in transplantation and link microbiota-immunity. Written for the highly successful Methods in Molecular Biology series, chapters feature the kind of detail and key implementation advice for best results in the lab. Authoritative and up-to-date, Cytotoxic T-Cells: Methods and Protocols, Second Edition serves as an ideal guidefor researchers working with these vital cells.

This detailed book highlights recent advances in molecular imaging techniques and protocols, designed to be immediately applicable in global bio-laboratories. The chapters are categorized into seven major groups according to the reporter materials, such as imaging with passive optical readouts, activatable bioluminescent probes, functional substrates and luciferases, organic fluorescent probes, BRET probes, FRET probes, as well as with advanced instrumentation. 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, Live Cell Imaging: Methods and Protocols aims to direct and inspire researchers into creating smarter, next-generation imaging techniques that are truly quantitative, highly sensitive, and readily comprehended, in the effort to engender deeper understanding of biological systems and break new ground in the research fields of life science.

This detailed volume presents a variety of animal models that are commonly used to study sepsis and some key procedures to measure specific disease outcomes. The chapters describe well-established surgical and nonsurgical rodent models of sepsis, presented by experts in the field. In addition, the book includes protocols for burn injury and sepsis, modeling the mouse intensive care unit (MICU), and the development of humanized mice, which may be useful tools to increase the translational potential of rodent sepsis research. There is a chapter discussing the use of biomarkers for sepsis diagnosis and prognosis in humans and mice, as well as chapters describing specific methods for biomarker measurement, and the use of analgesics and humane endpoints in rodent sepsis research. Finally, agent-based computational modeling is presented as a valuable complementary approach to study sepsis. 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, Sepsis: Methods and Protocols serves as an ideal guide for researchers working toward improving the identification and treatment of septic patients.

This volume explores analytical methods to study complex lipid mixtures from plants and algae. The chapters in this book are organized into five parts and cover topics such as basic methods of lipid isolation and analysis; mass spectrometry and NMR analysis; lipid isolation and analysis from plant tissues, cell compartments and organelles; lipid signaling, lipid-protein interactions, and imaging; and lipid databases. 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, Plant Lipids: Methods and Protocols is a valuable guide for experienced researchers and undergraduate, graduate, and Ph.D. students. This book is also an excellent resource for novice scientists with little to no experience inlipid experiments who are interested in approaching this field experimentally.

This detailed book focuses on cutting-edge methods for Parkinson¿s disease (PD) research, such as the analysis of the prion-like properties of ¿-synuclein, mitochondrial functions related to the PINK1-Parkin pathway/CHCHD2, the endolysosome pathway related to LRRK2, VPS35, and ATP13A2 using cultured cells (including patient iPS cells), deep brain stimulation therapy, classic mitochondrial toxins related to PD, and genetic associations and screenings using mammalian and invertebrate genetic models of PD. The collection intends to serve as an introductory protocol book for basic research on PD pathogenesis. 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, Experimental Models of Parkinson's Disease is an ideal guide for researchers continuing to work toward making PD risk predictable and surmountable.

This open access book explores techniques for working in the field of immunogenetics, i.e. fundamental and translational research into the adaptive immune receptor repertoire. Many chapters are dedicated to lab protocols, bioinformatics, and immunoinformatics analysis of high-resolution immunome analysis, exemplified by numerous applications. Additionally, the newest technological variations on these protocols are discussed, including non-amplicon, single-cell, and cell-free strategies. 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, Immunogenetics: Methods and Protocols covers a broad spectrum of methodologies for applications in research and clinical diagnostics to illustrate the impact that immunogenetics has achieved and will further expand in all fields of medicine, from infection and (auto)immunity, to vaccination, to lymphoid malignancy and tumor immunity.

This second edition volume details the latest aspects of neural cells covering the practical and theoretical considerations of each techniques involved. Chapters guide readers through a general overview of the neuronal culturing principles, cell line models for neural cells, the isolation and propagation of primary cultures, stem cells, transfection and transduction of neural cultures, and other more advanced techniques. 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. Practical and easy to use, Neuronal Cell Culture: Methods and Protocols, Second Edition aims to be of interest to scientists at all levels studying cell culture models for neuroscientific studies.

This volume explores the recent advances in the study of translational paths in central inflammation and focuses on ongoing pathophysiological processes and the transition between inflammatory stages and progressive states with neurodegeneration. Chapters cover topics such as pathophysiological hallmarks of neuroinflammation from tissue damage to reorganization; connecting studies of mouse models; and investigations of humans with multiple sclerosis. 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 practical, Translational Methods for Multiple Sclerosis Research is a valuable resource for researchers who want to learn more about this chronic ad progressive disease, and pave the way for new advancements.

This volume presents the most useful laboratory protocols in strigolactones(SL) research. Chapters guide readers through wet-lab paths, issues around stability, protocols to evaluate SL activity, effects towards soil inhabitants such as parasitic plants, mycorrhizal and non-mycorrhizal fungi, nodulating bacteria, and protocols to assess effects on plant development are discussed. 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, Strigolactones: Methods and Protocols aims to deliver a clear-cut and standardized set of experimental protocols to a broad scientific community.

This volume provides a wide range of imaging protocols that can be tailored to specific organisms or cell-types. Chapters guide readers through fixed-cell, live-cell, phenotype screening, super-resolution, intravital imaging techniques, and fluorescence life-time imaging microscopy (FLIM). 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, Confocal Microscopy: Methods and Protocols aims to ensure successful results in the further study of this vital field.

This second edition provides new and updated chapters detailing recent advances in MYC research and current techniques. Chapters guide readers through protocols on how to express and purify MYC protein, X-ray crystallography, NMR, techniques to study how MYC is modified, apoptosis, senescence, proliferation, metabolic changes, translation, tumorigenesis,reprogramming, and clinical application of MYC studies.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, The Myc Gene: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

This detailed book explores the fundamentals of myofibroblast biology in tissue repair, fibrosis, and tumors as well as providing cutting-edge laboratory methods used to investigate myofibroblast functions in physiological and pathological settings in vitro and in vivo, as written by leading academic scientists. Section I of this volume focuses on fundamental methods to study myofibroblast biology and covers topics such as methods for detecting myofibroblasts and senescent myofibroblasts in cell culture and histology, single cell RNA sequencing to identify myofibroblast subsets in fibrotic tissues, and functional assays to assess TGF-¿ activation, myofibroblast apoptosis, or matrix deposition and crosslinking. Section II discusses methods to investigate the mechanobiology of myofibroblasts in vitro, including the fabrication of functional hydrogels with tunable stiffness, the use of atomic force microscopy to characterize matrix and cellular stiffness, as well as molecular assays to assess fibroblast mechanotransduction pathways and durotaxis. Section III describes multiple animal models to investigate myofibroblast functions across organs in vivo as well as human organoid systems, precision tissue slices and decellularized 3D tissue scaffolds to assess myofibroblast functions in relevant human ex vivo models. 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 extensive, Myofibroblasts: Methods and Protocols is an essential collection for researchers delving into the processes and effects of these important cells.

This second edition volume expands on the previous edition with updated chapters in model systems and new crops. The book contains protocols for plastid engineering in leaves, tissue culture cells, and the shoot apex of plants, as well as for marker excision from the plastid genome and engineering Rubisco, the key enzyme of photosynthesis. 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, Chloroplast Biotechnology: Methods and Protocols, Second Edition is a valuable resource for researchers who wish to enter the field, and for practitioners looking for insights of applications in agriculture, industrial biotechnology and healthcare.

This volume provides readers with a comprehensive look at the latest techniques used to identify and characterize PDZ-mediated interactions. Chapters cover topics such as promiscuity, multimodularity, regulation, and viral recognition by PDZ domains. 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, PDZ Mediated Interactions: Methods and Protocols is a valuable resource for all researchers interested in learning more about this developing field.

This volume provides methods and protocols on principle, production, molecular aspects, and sustainability of biofuel and biodiesel. Chapters are divided into four sections detailing biofuel production, biodiesel production, molecular genetics, biotechnology of biofuel and biodiesel production, economics, and sustainability of biofuel production. 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, Biofuels and Biodiesel aims to be useful for researchers, students, and enthusiasts in the field of biofuel and biodiesel.

This detailed book collects modern and established computer-based methods aimed at addressing the drug discovery challenge from disparate perspectives by exploiting information on ligand-protein recognition. Beginning with methods that allow for the exploration of specific areas of chemical space and the designing of virtual libraries, the volume continues with sections on methods based on docking, quantitative models, and molecular dynamics simulations, which are employed for ligand discovery or development, as well as methods exploiting an ensemble of protein structures for the identification of potential protein targets. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Protein-Ligand Interactions and Drug Design provides detailed practical procedures of solid computer-aided drug design methodologies employed to rationalize and optimize protein-ligand interactions, for experienced researchers and novices alike.

This volume explores methods and protocols for detecting epistasis from genetic data. Chapters provide methods and protocols demonstrating approaches to identify epistasis, genetic epistasis testing, genome-wide epistatic SNP networks, epistasis detection through machine learning, and complex interaction analysis using trigenic synthetic genetic array (¿-SGA). Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Epistasis: Methods and Protocols aims to ensure successful results in the further study of this vital field. "Simulating Evolution in Asexual Populations with Epistasis¿ is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This extensive book brings together leading melanoma researchers from across the world and highlights many of the cutting-edge protocols and experimental systems currently being used to investigate questions surrounding this disease. The volume opens with sections on 2D and 3D cell culture-based approaches for studying melanoma biology, and continues with collections of chapters examining various approaches for detecting, isolating, and characterizing circulating melanoma cells, circulating tumor DNA, and exosomes, as well as experimental procedures for studying and detecting melanoma metastasis in both pre-clinical and clinical settings, bioinformatics-based approaches, protocols for quantifying and characterizing immune cell infiltrates in both melanoma tumors and tertiary lymphoid structures, and development and evaluation of therapeutic strategies for melanoma treatment. 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 comprehensive, Melanoma: Methods and Protocols aims to serve basic research scientists and clinicians who bring questions from the clinic into the lab in order to translate observations in the laboratory into improved patient care for this highly malignant form of cancer.Chapter 14 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This volume looks at in vitro disease models representing the respiratory, hepatobiliary, osteochondral, nervous, dermal, ocular, immune system, and pathological biological processes like tumorigenesis for stem cell research. The chapters in this book cover a range of diseases and application of various stem cells such as adult stem cells and iPS. Chapters also discuss new methods to characterize and manipulate stem cells with the aim to better understand and improve their biological performance. 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, In Vitro Models for Stem Cell Therapy: Methods and Protocols is a valuable resource for researchers and scientists interested in learning more about this exciting field