Böcker i Methods in Molecular Biology-serien

This volume covers a wide range of approaches utilized to decipher cellular and molecular mechanisms that contribute to successful nerve regeneration leading to functional recovery. Chapters detail a variety of models utilizing both in vivo and in vitro approaches, physical injury models, methods for the isolation/analysis of various macromolecules, live and fixed imaging of regenerating axons, and for quantifying behavioral endpoints enable measurements of regenerative success. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Axon Regeneration: Methods and Protocols aims to be comprehensive guide for researchers.

This second edition volume expands on the previous edition with discussions on the latest approaches used in the spectral cytometry field. Beginning with a brief history of spectral cytometry development, this book continues with a section addressing new protocols in different areas of imaging cytometry based on the unique technology of Imagestream and also introduces FlowCam ¿ cytometer with capabilities of analyzing phytoplankton and zooplankton. Written for the highly successful Methods in Molecular Biology series, chapters include brief introductions to their respective topics, complete lists of the materials and reagents necessary, and reproducible laboratory protocols with tips on troubleshooting and recommendations.Cutting-edge and thorough, Spectral and Imaging Flow Cytometry: Methods and Protocols, Second Edition is a valuable resources for beginners and professionals interested in learning more about this developing field. Chapters 1, 2, and 5 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This detailed volume provides a robust set of methods to understand variation between patients with ovarian cancers, in vitro models to better study different stages of the disease, and in vivo models to test therapies. Beginning with clinical perspectives to orient basic scientists, the book continues with sections exploring methods to characterize features of the tumor microenvironment (TME), techniques to isolate cells for in vitro study, and in vitro and in vivo models to study the 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, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Ovarian Cancer: Methods and Protocols serves as an ideal guide for researchers seeking to improve their study of ovarian cancer and find newtherapeutic approaches.

This volume looks at the latest technologies and methods--combined with new genetic tools available in animal models--used in this constantly evolving field. The chapters in this book are organized into three sections: Section one covers muscle stem cells and progenitor cells; Section Two discusses animal models for muscle stem cells and regeneration; and Section Three explores bioinformatics and imaging analysis for muscle stem cells. 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, Skeletal Muscle Stem Cells and Regeneration: Methods and Protocols is a valuable tool for all researchers looking to expand their knowledge on skeletal muscle growth, repair, degeneration, aging, and regenerative medicine.

This volume explores techniques used to study and understand the latest research on pyroptosis. The chapters in this book cover topics such as experimental methods to induce pyroptosis via inflammasomes; approaches to identifying inflammasome activation in humans; ways to induce and detect pore formation; and techniques to evaluate cellular outcomes of pyroptotic cell death. 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, Pyroptosis: Methods and Protocols is a valuable tool for researchers who want to expand their knowledge of this developing field. It will be especially beneficial for those working in the fields of immunology, cancer biology, microbiology, and cell biology.

This volume details state-of-art eQTL analysis, where interdisciplinary researchers are provided both theoretical and practical guidance to eQTL analysis and interpretation.

This volume looks at the latest technologies and methods used by researchers to study mechanisms that control the aspects of plant stem cell signaling events.

Animal Cell Biotechnology: Methods and Protocols, Fourth Edition constitutes a comprehensive manual of state-of-the-art techniques for setting up mammalian cell lines and media for development of biopharmaceuticals, and optimizing critical parameters for cell culture considering the whole cascade from the lab to the final production.

This fully revised book includes new and improved protocols to analyze toxicity at the DNA, RNA, and protein levels using genomic, epigenomic, transcriptomic, and proteomic approaches. Sections of the book address key subjects such as bioinformatics and biostatistics, toxicant-induced lung inflammation and tumors, analysis of protein and gene expression and silencing, gene promoter methylation, detection of chromosomal and genome-wide damage, analysis of DNA-adducts and surrogate gene mutations, detection and characterization of cancer gene mutation, and many other areas of study. 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. Comprehensive and up-to-date, Molecular Toxicology Protocols, Third Edition will prove to play an important role in generating a better understanding of the field of toxicology and its sub-disciplines.

This book provides a comprehensive guide to scientists, engineers, and students that employ metabolomics in their work, with an emphasis on the understanding and interpretation of the data. Chapters guide readers through common tools for data processing, using database resources, major techniques in data analysis, and integration with other data types and specific scientific domains. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, practical guidance of methods and techniques, useful web supplements, and connect the steps from experimental metabolomics to scientific discoveries.Authoritative and cutting-edge, Computational Methods and Data Analysis for Metabolomics to ensure successful results in the further study of this vital field.

This book provides a comprehensive collection of classic and cutting-edge methodologies as well as bioinformatics and genome-editing approaches that are used to quantify immune mediators and analyze their function and biological activity in cancer cells and tissues.

This volume provides current and new advanced methods and protocols to study T cells. Chapters guide readers through T cell diversity using mass cytometry, analyzing T cells from single cell level, CRISPR/Cas9 techniques to study the T cell activation, techniques to study subsets of TcellΓÇÖs, procedures to study artificial antigen presentosomes for T cell activation, techniques to study the T cell development, two-photon microscopy, and MAIT cells. 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, T-Cell Receptor Signaling: Methods and Protocols aims to provide a wide range of approaches and be an invaluable resource for present and future generations of T cell researchers.

This volume looks at the latest techniques used to perform comparative structure analyses, and predict and evaluate protein-ligand interactions. The chapters in this book cover tools and servers such as LiteMol; Bio3D-Web; DALI; CATH; HoTMuSiC, a contact-base protein structure analysis tool known as CAD-Score; PyDockSaxs and HADDOCK; CombDock and DockStar; the BioMagResBank database; as well as BME and CoNSEnsX+. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls.Cutting-edge and comprehensive, Structural Bioinformatics: Methods and Protocols is a practical guide for researchers to learn more about the aforementioned tools to further enhance their studies in the growing field of structural bioinformatics.Chapter 13 is available open access under a CC-BY 4.0 license via link.springer.com.

This second edition provides techniques used to study of the underlying transcriptional programs of stem cells that promote self-renewal and differentiation. Chapters detail next-generation sequencing technologies, data analysis, protocols on analysis and visualization of single-cell RNA-Seq data, analysis of 3D chromatin architecture, interpretation of large-scale interaction networks, transcriptional networks in embryonic and adult stem cells, derivation of stem cells, and transcriptional programs that promote reprogramming, transdifferentiation, and cancer formation. 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, Stem Cell Transcriptional Network: Methods and Protocols, Second Edition aims to provide a key resource for biologists seeking to interrogate these vital networks.

This volume details protocols encompassing different aspects of computer aided design and manufacturing of 3D scaffolds and biofabricated constructs for tissue engineering applications.

This volume details protocols encompassing different aspects of computer aided design and manufacturing of 3D scaffolds and biofabricated constructs for tissue engineering applications.

This volume explores homologous recombinationΓÇÖs (HR) essential role in meiotic and somatic cells. It discusses the analysis of different steps of the HR process from the genetic, molecular biology, and cell biology perspectives. Using a variety of model systems, chapters in this book cover topics such as the genome-wide mapping of DNA double-strand breaks (DSB); analysis of DNA-end resection and recombination intermediates by gel electrophoresis and southern blotting; cell-based monitoring of HR activity in meiotic and mitotic cells; in vitro analysis of branch migration, DNA strand exchange and Holliday junction resolution; or super resolution imaging of HR repair at collapsed replication forks. 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, Homologous Recombination: Methods and Protocols is a valuable resource that uses both classical and more recent approaches to answer questions on the HR mechanism. It is a useful tool for scientists working on the field of genome integrity, as well as those working in cancer biology and DNA repair. 

Preface...Table of Contents...Contributing Authors...1Detection of DNA Double Strand Breaks by γ-H2AX ImmunodetectionSonia I. Barroso and Andrés Aguilera 2END-seq: An Unbiased, High-Resolution and Genome-Wide Approach to Map DNA Double Strand Breaks and Resection in Human CellsNancy Wong, Sam John, André Nussenzweig, and Andres Canela3Resection of a DNA Double-Strand Break by Alkaline Gel Electrophoresis and Southern BlottingErika Casari, Elisa Gobbini, Michela Clerici, and Maria Pia Longhese4Analysis of DNA Double-Strand Break Ends Resection and Single-Strand Annealing in S. pombeZhenxin Yan, Sandeep Kumar, and Grzegorz Ira5Quantifying DNA End Resection in Human CellsYi Zhou and Tanya T. Paull6Genetic and Molecular approaches to Study Chromosomal Breakage at Secondary Structure-Forming RepeatsAnissia Ait Saada, Alex Costa, and Kirill S. Lobachev7Biochemical analysis of D-Loop Extension and DNA Strand Displacement SynthesisYoungho Kwon and Patrick Sung8DNA Strand Exchange to Monitor Human RAD51-Mediated Strand Invasion and PairingSudipta Lahiri and Ryan B. Jensen9Monitoring Homologous Recombination Activity in Human CellsDomagoj Vugic, Åsa Ehlén, and Aura Carreira10Inter-Homolog Homologous Recombination in Mouse Embryonic Stem CellsFabio Vanoli, Rohit Prakash, Travis White, and Maria Jasin11Branch Migration Activity of Rad54 ProteinOlga M. Mazina and Alexander V. Mazin12Holliday Junction ResolutionRaquel Carreira, F. Javier Aguado, Tomas Lama-Diaz, and Miguel G. Blanco13Identification and Analysis of Different Types of UFBsSimon Gemble and Mounira Amor-Guéret14Intrachromosomal Recombination in YeastAnastasiya Epshtein, Lorraine S. Symington, and Hannah L. Klein15Genome-Wide Analysis of Mitotic Recombination in Budding YeastLydia R. Heasley, Nadia M. V. Sampaio, and Juan Lucas Argüeso16Monitoring Gene Conversion in Budding Yeast by Southern Blot AnalysisMiyuki Yamaguchi and James E. Haber17DNA Double-Strand Break Induced Gene Amplification in YeastTomas Strucko, Michael Lisby, and Uffe Hasbro Mortensen18Measuring Chromosome Pairing during Homologous Recombination in YeastFraulin Joseph, So Jung Lee, Eric Bryant, and Rodney Rothstein19Cytological Monitoring of Meiotic Crossovers in Spermatocytes and OocytesYan Yun, Masaru Ito, Sumit Sandhu, and Neil Hunter20Detection of DSBs in C. elegans MeiosisTatiana García-Muse21Methods to Map Meiotic Recombination Proteins in Saccharomyces cerevisiaeAurore Sanchez and Valérie Borde22Investigation of Break-Induced Replication in YeastBeth Osia, Rajula Elango, Juraj Kramara, Steven A. Roberts, and Anna Malkova23Measurement of Homologous Recombination at Stalled Mammalian Replication ForksNicholas A. Willis and Ralph Scully24Super Resolution Imaging of Homologous Recombination Repair at Collapsed Replication ForksDonna R. Whelan and Eli Rothenberg25The Analysis of Recombination-Dependent Processing of Blocked Replication Forks by Bi-Dimensional Gel ElectrophoresisKarol Kramarz, Anissia Ait Saada and Sarah A.E. Lambert26The Sister Chromatid Exchange Assay in Human CellsEmanuela Tumini and Andrés Aguilera27Analysis of Recombination at Yeast TelomeresMarie-Noelle Simon, Dmitri Churikov and Vincent Géli28Gel Electrophoresis Analysis of rDNA Instability in Saccharomyces cerevisiaeMariko Sasaki and Takehiko Kobayashi29Analyzing Homologous Recombination at a Genome Wide LevelColine Arnould, Vincent Rocher, and Gaëlle Legube30CRISPR/Cas9 Induced Breaks in Heterochromatin, Visualized by ImmunofluorescenceMitrentsi Ioanna and Evi Soutoglou31In Vivo Binding of Recombination Proteins of Non

This detailed book collects methods based on the evolution of the chromosome conformation capture (3C) technique and other complementary approaches to dissect chromatin conformation with an emphasis on dissection of nuclear compartmentalization and visualization in imaging.

This detailed book collects methods based on the evolution of the chromosome conformation capture (3C) technique and other complementary approaches to dissect chromatin conformation with an emphasis on dissection of nuclear compartmentalization and visualization in imaging.

Beginning with a section on computational design of target-specific guide RNAs, the book continues by covering chemical modifications to alter guide RNA stability, specificity, and efficiency, as well as to create inducible guide RNAs, append additional functional domains, and express guide RNAs in a conditional manner.

Beginning with a section on computational design of target-specific guide RNAs, the book continues by covering chemical modifications to alter guide RNA stability, specificity, and efficiency, as well as to create inducible guide RNAs, append additional functional domains, and express guide RNAs in a conditional manner.