Böcker utgivna av Springer-Verlag New York Inc.

This volume describes a range of standard and novel methodological approaches used to probe ion channel function across different modalities. Chapters guide readers through methods and protocols from an introduction to the decades old patch clamp method for the ion channel neophyte to more complex, recent protocol advances, such as optogenetics. 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 practical, Patch Clamp Electrophysiology:  Methods and Protocols aims to be a reference guide for current and future ion channel physiologists. 

Foreword...Preface...Table of Contents...Contributing Authors...1.Isolation and Analysis of Lipid Rafts from Neural Cells and TissuesSara Grassi, Paola Giussani, Laura Mauri, Simona Prioni, and Alessandro Prinetti2.A Detergent-Free Method for Preparation of Lipid Rafts for the Shotgun Lipidomics StudyChao Qin, Meixia Pan, and Xianlin Han3. Biochemical Analysis of Lipid Rafts to Study Pathogenic Mechanisms of Neural DiseasesErnesto R. Bongarzone and Maria Irene Givogri4. Amyloid- ╬▓ Interactions with Lipid Rafts in Biomimetic Systems: A Review of Laboratory MethodsGalya Staneva, Chiho Watanabe, Nicolas Puff, Vesela Yordanova, Michel Seigneuret, and Miglena Angelova5. Extracellular Vesicles Containing Ceramide-Rich Platforms: "Mobile Raft" Isolation and AnalysisAhmed Elsherbini, Haiyan Qin, Zhihui Zhu, Priyanka Tripathi, Guanghu Wang, Simone M. Crivelli, Stefanka D. Spassieva, and Erhard Bieberich6. Isolation of Lipid Rafts (Detergent-Resistant Microdomains) and Comparison to Extracellular Vesicles (Exosomes)Glyn Dawson7. Methods to Characterize Synthesis and Degradation of Sphingomyelin at the Plasma Membrane and Its Impact on Lipid Raft DynamicsMariana Nikolova-Karakashian8. Association of Glycolipids and Growth Factor Receptors in Lipid RaftsJing Wang and Robert K. Yu9. Lipid Raft Isolation by Sucrose Gradient Centrifugation and Visualization of Raft-Located Proteins by Fluorescence Microscopy: The Use of Combined Techniques to Assess Fas/CD95 Location in Rafts during Apoptosis TriggeringConsuelo Gajate and Faustino Mollinedo10. Elucidating the Role of Lipid Rafts on G Protein-Coupled Receptor Function in the Mouse Kidney: An In Vivo ApproachLaureano D. Asico, Selim Rozyyev, Annabelle M. Crusan, Pedro A. Jose, and Van Anthony M. Villar11. Analysis of Lipids in Ceramide-Enriched Membrane DomainsAlexander Carpinteiro and Erich Gulbins12. Chemotherapeutic Agents-Induced Ceramide Rich Platforms (CRPs) in Endothelial Cells and their ModulationPrerna R. Nepali and Adriana Haimovitz-Friedman13. Biophysical Analysis of Lipid Domains by Fluorescence MicroscopyAna E. Ventura, T├ónia C. B. Santos, Joaquim T. Marqu├¬s, Rodrigo F.M. de Almeida, and Liana C. Silva14. Biophysical Analysis of Lipid Domains in Mammalian and Yeast Membranes by Fluorescence SpectroscopyCarla Sousa, Filipa C. Santos, Andreia Bento-Oliveira, Beatriz Mestre, Liana C. Silva, and Rodrigo F. M. de Almeida15. Characterization of Lipid Order and Domain Formation in Model Membranes Using Fluorescence Microscopy and SpectroscopyAndrew Fuhrer and Amir M. Farnoud16. Characterization of the Effect of Sphingolipid Accumulation on Membrane Compactness, Dipole Potential, and Mobility of Membrane ComponentsGyula Batta, T├¡mea Hajdu, and Peter Nagy17. Super-Resolution Microscopy of SphingolipidsJan Schlegel and Markus Sauer18. Detection of Functionalized Sphingolipid Analogues in Detergent Resistant Membranes of the Immune Cells  Julian Fink, J├╝rgen Seibel, and Elita Avota19. Immunofluorescence Labeling of Lipid-Binding Proteins CERTs to Monitor Lipid Rafts DynamicsCaterina Giovagnoni, Simone M. Crivelli, Mario Losen, and Pilar Martinez-Martinez20. Cross-Link/Proximity Ligation Assay for Visualization of Lipid and Protein Complexes in Lipid RaftsPriyanka Tripathi, Zhihui Zhu, Haiyan Qin, Ahmed Elsherbini, Emily A. Roush, Simone M. Crivelli, Stefanka D. Spassieva, and Erhard BieberichSubject Index List...

This volume gives a comprehensive insight into established and novel methods to analyze the structure and function of lipid rafts. This book covers topics such as isolation of lipid rafts and their functional analysis using biochemical methods; visualization of lipid rafts and their interaction with proteins using fluorescence-related methods; preparation of giant lipid vesicles and fluorescence spectroscopy; FRET and FRAP; and using photo-activated cross-linking of a ceramide analog combined with proximity ligation assay. 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, Lipid Rafts: Methods and Protocols is a valuable resource for both novice and expert researchers interested in learning more about the function of lipid rafts in many areas of cell biology and medicine. 

This detailed collection explores techniques involved in the main strategies of nanopore sensing, such as translocation, analyte trapping, and interactions with external binding sites. Opening with a section on nanopore design and nanopore production, the book continues with parts devoted to various biological nanopores, nanopore engineering, and their uses in single molecule sensing, computational methods to study intrinsic nanopore behavior, characterizing the specific translocation activity of a vesicle particle through a nanopore, as well as the use of the technique droplet interface bilayer (DIB) in nanopore and membrane biophysical studies. 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, Nanopore Technology: Methods and Protocols, with its focus on nanopore technology and biomolecule characterization, will hold the interest of the biophysicists, biochemists, bioengineers, and molecular biologists who are working toward further understanding this key field of research.

Part I: Design and Preparation of Biological Based Nanopores 1. Preparation of Fragaceatoxin C (FraC) Nanopores            Natalie Lisa Mutter, Gang Huang, Nieck van der Heide, Florian Leonardus Rudolfus Lucas, Nicole St├⌐phanie Galenkamp, Giovanni Maglia, and Carsten Wloka 2. Preparation of Cytolysin A (ClyA) Nanopores            Nicole St├⌐phanie Galenkamp, Veerle Van Meervelt, Natalie Lisa Mutter, Nieck van der Heide, Carsten Wloka, and Giovanni Maglia 3. Building Synthetic Transmembrane Peptide Pores            Kozhinjampara R. Mahendran 4. Design and Assembly of Membrane-Spanning DNA Nanopores            Kerstin G├╢pfrich and Ulrich F. Keyser Part II: Single Molecule Detection and Analysis of Protein Analytes 5. Determining the Orientation of Porins in Planar Lipid Bilayers            Sandra A Ionescu, Sejeong Lee, and Hagan Bayley 6. Revelation of Function and Inhibition of Wza through Single Channel Studies            Lingbing Kong 7. Protein Analyte Sensing with an Outer Membrane Protein G (OmpG) Nanopore            Monifa A.V. Fahie, Bib Yang, Christina M. Chisholm, and Min Chen 8. Nanopore Enzymology to Study Protein Kinases and their Inhibition by Small Molecules            Leon Harrington, Leila T. Alexander, Stefan Knapp, and Hagan Bayley 9. A Selective Activity-Based Approach for Analysis of Enzymes with an OmpG Nanopore            Monifa A.V. Fahie, Bach Pham, Fanjun Li, and Min Chen 10. Oligonucleotide-Directed Protein Threading through a Rigid Nanopore            Garbi├▒e Celaya and David Rodriguez Larrea 11. Unfolding and Translocation of Proteins through an Alpha-Hemolysin Nanopore by ClpXP            Jeff Nivala, Logan Mulroney, Qing Luan, Robin Abu-Shumays, and Mark Akeson Part III: Computational Analysis of Nanopore Behavior 12. Simulation of pH-Dependent, Loop-Based Membrane Protein Gating Using Pretzel            Alan Perez-Rathke, Monifa A.V. Fahie, Christina M. Chisholm, Min Chen, and Jie Liang 13. Free Energy Minimization for Vesicle Translocation through a Narrow Pore            Hamid R. Shojaei, Ahad Khaleghi Ardabili, and Murrugappan Muthukumar Part IV: Droplet Interface Bilayer System 14. Single Ion-Channel Analysis in Droplet Interface Bilayer            Arash Manafirad 15. Continuous and Rapid Solution Exchange in a Lipid Bilayer Perfusion System Based on Droplet-Interface Bilayer            En-Hsin Lee 16. Protein Transport Studied by a Mo

This volume discusses the vaccine development process and the role delivery concepts contribute to a global goal of effective health outcomes.

This volume discusses the vaccine development process and the role delivery concepts contribute to a global goal of effective health outcomes.

1. Next day Salmonella spp. Detection Method Based on real-time PCR for FoodsDavid Rodr├¡guez-L├ízaro and Marta Hern├índez 2. Isolation of Salmonella spp. from Animal FeedKM Feye, AE Powell, Blaine Booher, Zachary Flores, PM Rubinelli, LH Calderwood, KE Richardson, PA Davis, R Sellers, and SC Ricke3. Investigating Outbreaks of Salmonella Typhimurium using Case-control Studies, with a Reference to the One Health ApproachKatrin Gaardbo Kuhn and Steen Ethelberg 4. Detection of Salmonella by the 3M Molecular Detection Assays - MDS┬« MethodGreici Bergamo and Eliezer Avila Gandra 5. CRISPR-Typing of Salmonella IsolatesNikki Shariat and Edward Dudley 6. CRISPR Typing of Salmonella Isolates from Different ResourcesQiuchun Li 7. Immunomagnetic Separation of Salmonella with Tailored Magnetic Micro and NanocarriersMar├¡a Isabel Pividori  8. Self-labeling Enzyme Tags for Translocation Analyses of Salmonella Effector Proteins Vera G├╢ser and Michael Hensel   9. Smartphone Based Paper Microfluidic Immunoassay of Salmonella and E. coli Laurel Dieckhaus, Tu San Park, and Jeong-Yeol Yoon  10. Correlative Light and Scanning Electron Microscopy to Study Interactions of Salmonella enterica with Polarized Epithelial Cell Monolayers Carina Kommnick and Michael Hensel  11. Production of Murine Macrophages from Hoxb8-immortalized Myeloblasts: Utility and use in the Context of Salmonella InfectionZiyan Fang, Margaux Lagier, and St├⌐phane M├⌐resse 12. In vitro Evaluation of Anti-biofilm Agents Against Salmonella entericaJenna Sandala and John S. Gunn 13. Generation of Random luxCDABE Transcripcional Fusions in the Genome of Salmonella entericaJuan J. de la Rosa-Altura, Barbora Benesova, Concepci├│n Panadero-Medianero, Aida Amador-├ülvarez, Julia Aguilera-Herce, Juan Luis Araujo-Garrido, Joaqu├¡n Bernal-Bayard, and Francisco Ramos-Morales 14. Vaccine Based On Outer Membrane Vesicles Using Hydrogels as Vaccine Delivery SystemYadira Pastor, Isaiah Ting, Melibea Berzosa, Juan M. Irache, and Carlos Gamazo15. Detection and Characterization of Salmonella enterica Serotypes by Simple PCR TechnologiesSamuel Kariuki and John Kiiru 16. Determination of Antimicrobial Resistance of Salmonella in PorkJing Wang and Dan Gu 17. Molecular typing of Salmonella by Pulsed-field Gel ElectrophoresisXilong Kang, Chuang Meng, and Zhiming Pan 18. Isolation and Identification of Salmonella in PorkHongqin Song and Aihua Zhu

1. Substitutional RNA Editing in Plant OrganellesMizuho Ichinos and Mamoru Sugita 2. Computational Detection of Plant RNA Editing EventsAlejandro A. Edera and M. Virginia Sanchez-Puerta 3. Discovering RNA Editing Events in FungiHuiquan Liu and Jin-Rong Xu 4. C-to-U RNA Editing: From Computational Detection to Experimental ValidationTaga Lerner, Mitchell Kluesner, Rafail Nikolaos Tasakis, Branden S. Moriarity, F.N. Papavasiliou, and  Riccardo Pecori 5. Live Cell Quantification of APOBEC1-mediated RNA Editing: A Comparison of RNA Editing AssaysMartina Chieca, Serena Torrini, and  Silvestro G. Conticello 6. Adenosine to Inosine RNA Editing Enzyme ADAR and microRNAsKang Yuting, Dan Ding, and Hisashi Iizasa 7. Quantitative Analysis of Adenosine-to-Inosine RNA EditingTurnee N. Malik, Jean-Philippe Cartailler, and Ronald B. Emeson 8. Discovering A-to-I RNA Editing Through Chemical MethodsMasayuki Sakurai, Shunpei Okada, Hiroki Ueda, and Yang Yuxi 9. ALU A-to-I RNA Editing - Millions of Sites and Many Open QuestionsAmos Schaffer and Erez Y. Levano 10. RNA Editing in Human and Mouse TissuesHarini Srinivasan, Eng Piew Louis Kok, and Meng How Tan 11. Bioinformatics Resources for RNA EditingMaria Angela Diroma, Loredana Ciaccia, Graziano Pesole, and Ernesto Picardi  12. High-throughput Sequencing to Detect DNA-RNA Changes Claudio Lo Giudice, Graziano Pesole, and Ernesto Picardi 13. Detection of A-to-I Hyper-Edited RNA SequencesRoni Cohen-Fultheim and Erez Y. Levanon   14. Proteome Diversification by RNA EditingEli Eisenberg 15. MicroRNA Editing Detection and Function: A Combined in silico and Experimental Approach for the Identification and Validation of Putative Oncogenic TargetsValentina Tassinari, Valeriana Cesarini, Domenico Alessandro Silvestris, Andrea Scafidi, Lorenzo Cucina, and Angela Gallo 16. RNA Editing in InterferonopathiesLoredana Frassinelli, Silvia Galardi, Silvia Anna Ciafr├¿, and Alessandro Michienzi 17. The Role of RNA Editing in the Immune ResponseSadeem Ahmad, Xin Mu, and Sun Hur 18. RNA Editing in Neurological and Neurodegenerative DisordersPedro Henrique Costa Cruz and Yukio Kawahara 19. New Frontiers for Site-directed RNA Editing - Harnessing Endogenous ADARsTobias Merkle and Thorsten Stafforst 

This third edition expands upon the previous edition with current, detailed methods on different aspects, and landmarks advancing knowledge on Salmonella research. With new chapters on molecular assays for detection, identification and serotyping of Salmonella, quantitative proteomic identification of host factors involved in salmonella infection, determination of antimicrobial resistance in salmonella, site-directed mutagenesis, chromosomal gene analysis, various microscopy methods to analyze salmonella interaction with host cells, in vitro modeling of gallbladder-associated salmonella colonization, and analysis of salmonella phages and prophages. 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, Salmonella: Methods and Protocols, Third Edition aims to provide methods that will have an impacted Salmonella research

Part I: Fundamental Aspects of Cryopreservation and Freeze-Drying 1. Principles Underlying Cryopreservation and Freeze-Drying of Cells and Tissues            Willem F. Wolkers and Harri├½tte Oldenhof 2. Principles of Ice-Free Cryopreservation by Vitrification            Gregory M. Fahy and Brian Wowk 3. The Principles of Freeze-Drying and Application of Analytical Technologies            Kevin R. Ward and Paul Matejtschuk 4. Mathematical Modeling and Optimization of Cryopreservation in Single Cells            James D. Benson 5. Mathematical Modeling of Protectant Transport in Tissues            Ross M. Warner and Adam Z. Higgins Part II: Technologies and Methods to Study Freezing and Drying 6. Freezing Technology: Control of Freezing, Thawing, and Ice Nucleation            Peter Kilbride and Julie Meneghel 7. Microwave- and Laser-Assisted Drying for the Anhydrous Preservation of Biologics            Shangping Wang, Susan Trammell, and Gloria D. Elliott 8. High-Speed Video Cryomicroscopy for Measurement of Intracellular Ice Formation Kinetics            Jens O.M. Karlsson 9. Use of Ice Recrystallization Inhibition Assays to Screen for Compounds that Inhibit Ice Recrystallization            Anna A. Ampaw, August Sibthorpe, and Robert N. Ben 10. DSC Analysis of Thermophysical Properties for Biomaterials and Formulations            Wendell Q. Sun 11. Osmometric Measurements of Cryoprotective Agent Permeation into Tissues            Kezhou Wu, Leila Laouar, Nadia Shardt, Janet A.W. Elliott, and Nadr M. Jomha 12. Use of X-Ray Computed Tomography for Monitoring Tissue Permeation Processes            Ariadna Corral, Alberto Olmo, and Ram├│n Risco 13. Use of In Situ Fourier Transform Infrared Spectroscopy in Cryobiological Research            Willem F. Wolkers and Harri├½tte Oldenhof 14. Raman Cryomicroscopic Imaging and Sample Holder for Spectroscopic Subzero Temperature Measurements            Guanglin Yu, Rui Li, and Allison Hubel Part III: Cryopreservation and Freeze-Drying Protocols 15. Cryopreservation of Semen from Domestic Livestock: Bovine, Equine, and Porcine Sperm            Harri├½tte Oldenhof, Willem F. Wolkers, and Harald Sieme 16. Cryopreservation of Avian Semen            Henri Woelders 17. Cryopreservation of Mouse Sperm for Genome Banking            Y

This volume provides an overview about main RNA editing mechanisms, focusing on their functions in physiological as well as pathological conditions. Chapters guide readers through state- of-the art methodologies to investigate RNA editing through wet and dry approaches. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.Authoritative and cutting-edge, RNA Editing: Methods and Protocols aims to ensure successful results in the further study of this vital field. 

This fourth edition explores fully up-to-date standardly used cryopreservation, vitrification, and freeze-drying protocols for specimens that are used for research purposes, conservation of genetic reserves, and applications in agriculture and medicine. Beginning with a section on the fundamentals as well as the use of mathematical modeling to solve cryobiological problems, the book continues with sections on technological aspects of freezing and drying, analytical methods to study protectant loading of cells and tissues, cell behavior during freezing and drying, and thermodynamic properties of preservation solutions, as well as cryopreservation, vitrification, and freeze-drying protocols for a wide variety of samples and different applications. 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. Thorough and authoritative, Cryopreservation and Freeze-Drying Protocols, Fourth Edition serves as an ideal guide for researchers and technical assistants in academia and industry with a background in life sciences, medicine, or engineering who want to investigate freezing and drying of biological systems or set up methods to safely store biological specimens while maintaining their function upon reconstitution.The chapter ΓÇ£Freezing Technology: Control of Freezing, Thawing, and Ice NucleationΓÇ¥ is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This volume details a comprehensive range of methods for imaging epithelial-to-mesechymal transition (EMT)/MET in in vivo systems, and methods to leverage these systems to dissect the underlying mechanisms.

This volume details a comprehensive range of methods for imaging epithelial-to-mesechymal transition (EMT)/MET in in vivo systems, and methods to leverage these systems to dissect the underlying mechanisms.

This fully updated edition provides the most recent advances in cancer cell signaling knowledge combined with some discussion of the current challenges and prospects in cancer therapy.

This fully updated edition provides the most recent advances in cancer cell signaling knowledge combined with some discussion of the current challenges and prospects in cancer therapy.

It includes detailed techniques to examine mRNAs, small non-coding RNAs, protein-associated small RNAs, organelle RNAs, endosymbiont RNAs, and alternatively spliced RNA variants from various organisms.

It includes detailed techniques to examine mRNAs, small non-coding RNAs, protein-associated small RNAs, organelle RNAs, endosymbiont RNAs, and alternatively spliced RNA variants from various organisms.

Part I: Ribozyme Function1. Conjugation as a Highly Sensitive Assay to Study Group II Intron Splicing in vivoF├⌐lix LaRoche-Johnston, Caroline Monat, and Benoit Cousineau 2. Co-transcriptional Analysis of Self-cleaving Ribozymes and their Ligand DependenceLuiz F. M. Passalacqua and Andrej Lupt├ík Part II: Ribozyme Indentification and Characterization 3. Cloning and Detection of Genomic Retrozymes and their circRNA IntermediatesAmelia Cervera and Marcos de la Pe├▒a 4. Demonstration of a Ribozyme in Epsilon Domain of Hepatitis B Virus RNADibyajnan Chakraborty and Sagarmoy Ghosh 5. In vitro Selection of Varkud Satellite Ribozyme Variants that Cleave a Modified Stem-loop SubstratePierre Dagenais and Pascale Legault 6. Characterization and Optimization of a Deoxyribozyme with a Short Left Binding ArmYueyao Wang and Hanyang Yu 7. Computer-aided Design of Active Pseudoknotted Hammerhead RibozymesSabrine Najeh, Kasra Zandi, Samia Djerroud, Nawwaf Kharma, and Jonathan Perreault 8. Inverse RNA Folding Workflow to Design and Test Ribozymes Including PseudoknotsMohammad Kayedkhordeh, Ryota Yamagami, Philip C. Bevilacqua, and David H. Mathews Part III : Ribozyme Structure9. Using an L7Ae-tethered, Hydroxyl Radical-Mediated Footprinting Strategy to Identify and Validate Kink-Turns in RNAsStella M. Lai and Venkat Gopalan 10. SHAPE Profiling to Probe Group II Intron Conformational Dynamics during SplicingTimothy Wiryaman and Navtej Toor  11. Dynamics-Function Analysis in Catalytic RNA Using NMR Spin Relaxation and Conformationally Restricted NucleotidesCharles G. Hoogstraten, Montserrat Terrazas, Anna Avi├▒├│, Neil A. White, and Minako Sumita Part IV : Ribozyme Conjugations12. Design and Evaluation of Guide RNA Transcripts with a 3''-terminal HDV Ribozyme to Enhance CRISPR-based Gene InactivationBen Berkhout, Zongliang Gao and Elena Herrera-Carrillo 13. Design and Evaluation of AgoshRNAs with 3''-terminal HDV Ribozymes to Enhance the Silencing ActivityBen Berkhout and Elena Herrera-Carrillo 14. Cloning and Detection of Aptamer-ribozyme ConjugationsRyan P. Goguen, Anne Gatignol, and Robert J. Scarborough Part V: Ribozyme as Tools to Study other RNAs15. Use of a Lariat Capping Ribozyme to Study Cap Function in VivoMax Pietschmann, Gregor Tempel, Maral Halladjian, Nicolai Krogh, and Henrik Nielsen 16. Long Non-coding RNA Depletion using Self-cleaving RibozymesAlex C Tuck and Marc B├╝hler

This volume provides protocols designed to study the function and the structure of diverse ribozymes. Chapters guide readers through different techniques to identify and characterize new ribozymes and methods to use ribozymes to alter the function of CRISPR-based guide RNAs, AgoshRNAs and aptamers or to study RNA capping and long non-coding 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 tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Ribozymes: Methods and Protocols aims to help in accelerating ribozyme research and inspiring others to develop new methods to study ribozyme structure and function.

Part I: Introduction and Historical Background1. Paradigm Shifts in Mast Cell and Basophil Biology and Function: An Emerging View of Immune Regulation in Health and DiseaseAna Olivera and Juan Rivera Part II: Obtaining the Cells: Purification, Culture, and Counting2. Purification of Basophils from Peripheral Human BloodFranco H. Falcone and Bernhard F. Gibbs 3. Mast Cell Purification ProtocolsJasmine Farrington, Elizabeth P Seward, and Peter T Peachell 4. Generation of a Human Allergic Mast Cell Phenotype from CD133+ Stem CellsHans J├╝rgen Hoffmann 5. Generation and Culture of Peripheral CD34+ Stem Cell-derived Mast Cells (PSCMCs)Yanyan Luo, Stefan Frischbutter, J├╢rg Scheffel, and Frank Siebenhaar 6. Modulating the Human Basophil Phenotype During its Development and Maturation: Basophils Derived from in vitro Cultures of CD34+ Progenitor CellsDonald MacGlashan Jr. 7. Generation of Mast Cells from Murine Stem Cell ProgenitorsEmily J. Swindle 8. Integration of the Human Dermal Mast Cell into the Organotypic Co-culture Skin ModelJonghui Kim, Sven Guhl, Magda Babina, Torsten Zuberbier, and Metin Artuc 9. The Absolute Basophil CountElena Borzova Part III: Basophil/Mast Cell Lines10. Mast Cell and Basophils Cell Lines: A CompendiumEgle Passante 11. Use of Humanized RBL Reporter Systems for Detection of Allergen-specific IgE Sensitization in Human Serum Daniel Wan, Xiaowei Wang, Ryosuke Nakamura, Marcos J.C. Alcocer, and Franco H. Falcone 12. Use of Humanized Fluorescent Reporter Cell Line RBL NFAT-DsRed for Detection of Allergen-specific IgE in Patient Sera Using Allergen MicroarraysMarina Kalli, Marcos J. C. Alcocer, Andrew J. Blok, and Franco H. Falcone 13. NPY-mRFP Rat Basophil Leukemia (RBL) Reporter: A Novel, Fast Reporter of Basophil/Mast Cell Degranulation Nafal Barwary, Daniel Wan, and Franco H. Falcone 14. Use of Engineered Nanoparticles (ENPs) for the Study of High-affinity IgE Receptor Fc╬╡RI Receptor Engagement and Rat Basophil Leukemia (RBL) Cell degranulationAlelwani W, Alharbi RA , Wan D , Vllasaliu D, Falcone FH , and Stolnik S  Part IV: Diagnostic Applications 15. Flow Cytometric Allergy Diagnosis: Basophil Activation Techniques Chris H. Bridts, Vito Sabato, Christel Mertens, Margo M. Hagendorens, Luc S. De Clerck, and Didier G. Ebo 16. Basophil Activation Experiments in Immediate Drug Hypersensitivity: More Than a Diagnostic AidDidier G Ebo, Jessy Elst, Athina Van Gasse, Leander De Puysseleyr, Margaretha Faber, Margo M Hagendorens, Lina Mayorga, Christel Mertens , Chris H Bridts, Luc S De Clerck, and Vito Sabato 17. Basophil Activation Techniques: Staining of Exteriorized Granule Matrix Jessy Elst, Vito Sabato, Margo M Hagendorens, Michel van Houdt, Margaretha A. Faber, Chris H Bridts, Didier G Ebo, and Christel Mertens  18. Measurement and Functional Analysis of the Mas-related G protein-coupled receptor MRGPRX2 on Human Mast Cells and Basophils Jessy Elst, Vito Sabato, Margo M Hagendorens, Michel van Houdt, Margaretha A. Faber, Chris H Bridts, Didier G Ebo, and Christel Mertens 19. The Mast Cell Activation Test (MAT)Rajia Bahri and Silvia Bulfone-Paus Part V: Whole Cells: Functional Studies20. Quantity and Quality of Basophil RNA Depend on the RNA Extraction TechniqueVictor G. Bechmann, Anett

This second edition provides updated and new chapters to build on and extend the strengths of the first edition. Chapters guide readers through basic biology of basophils, obtaining the cells by purification, culture of stem cells progenitors, peripheral CD34+ stem cell-derived mast cells, basophils from CD34+ progenitors, diagnostic applications, gene expression patterns in basophils, roles of basophils in different asthma phenotypes, knockout, and disease models. 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, Basophils and Mast Cells: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

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.

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.

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 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. 

This volume details the fundamentals of the CRISPR-Cas system, and its protocols illustrate advances in CRISPR-Cas techniques for efficient genome editing. Introductory chapters provide a wide horizon of CRISPR/Cas-based methods and applications. Additional chapters guide readers through HDR-mediated editing, sgRNA design, the step-by-step procedure of multiplex adenine base editing experiments in rice, generating mutants for rice, wheat, Brachypodium, Barley, Flax, and Phytophthora, visual screening of mutants, gene deletion (knock-out), tagging (knock-in) in mammalian cells, the cloning-free (DNA-free) technique, cell-penetrating peptides, generating a genome-edited banana, and nuclear genome editing of Chlamydomonas employing CRISPR-Cpf1 combined with a single-stranded DNA (ssODN) repair template. Authoritative and cutting-edge, CRISPR-Cas Methods aims to assist researchers who are new to the field and are aiming to learn how best to adopt this technology for a particular organism.