Bücher veröffentlicht von Springer-Verlag New York Inc.

This second edition volume expands on the previous edition with discussions of recently developed techniques that use RNA scaffolds as molecular tools.

The book integrates mitochondria with other cellular components, discussing the dynamic properties of mitochondria with an emphasis on how these processes respond to signaling events and how they affect cellular metabolism.

Part I: Bioinformatic Tools to Study RNA Modifications 1. RNA Post-Transcriptional Modification Mapping Data Analysis Using RNA Framework            Ilaria Manfredonia and Danny Incarnato 2. An Informatics Pipeline for Profiling and Annotating RNA Modifications            Qi Liu, Xiaoqiang Lang, and Richard I. Gregory Part II: Detecting RNA Modifications Using Nanopore Direct RNA Sequencing 3. EpiNano: Detection of m6A RNA Modifications Using Oxford Nanopore Direct RNA Sequencing            Huanle Liu, Oguzhan Begik, and Eva Maria Novoa 4. Adaptation of Human Ribosomal RNA for Nanopore Sequencing of Canonical and Modified Nucleotides            Miten Jain, Hugh E. Olsen, Mark Akeson, and Robin Abu-Shumays Part III: Next-Generation Sequencing Approaches to Detect and Capture Modified RNAs 5. AlkAniline-Seq: A Highly Sensitive and Specific Method for Simultaneous Mapping of 7-Methyl-Guanosine (m7G) and 3-Methyl-Cytidine (m3C) in RNAs by High-Throughput Sequencing            Virginie Marchand, Lilia Ayadi, Val├⌐rie Bourguignon-Igel, Mark Helm, and Yuri Motorin 6. Transcriptome-Wide Detection of Internal N7-Methylguanosine            Li-Sheng Zhang, Chang Liu, and Chuan He 7. miCLIP-MaPseq Identifies Substrates of Radical SAM RNA Methylating Enzyme Using Mechanistic Crosslinking and Mismatch Profiling            Vanja Stojkovi─ç, David E. Weinberg, and Danica Galoni─ç Fujimori 8. Mapping RNA Modifications Using Photo-Crosslinking-Assisted Modification Sequencing            Bryan R. Cullen and Kevin Tsai 9. Quantitative and Single Nucleotide Resolution Profiling of RNA 5-Methylcytosine            Jun Li, Xingyu Wu, Trung Do, Vy Nguyen, Jing Zhao, Pei Qin Ng, Alice Burgess, Rakesh David, and Iain Searle 10. A Small RNA-Seq Protocol with Less Bias and Improved Capture of 2''-O-Methyl RNAs            Erwin L. van Dijk and Claude Thermes Part IV: Assessing RNA Modifications Using qPCR- and Molecular Biology-Based Methods 11. Assessing 2''-O-Methylation of mRNA Using Quantitative PCR            Brittany A. Elliott and Christopher L. Holley 12. Relative Quantification of Residue Specific m6A RNA Methylation Using m6A-RT-QPCR            Ane Olazagoitia-Garmendia and Ainara Castellanos-Rubio 13. Monitoring the 5-Methoxycarbonylmethyl-2-Thiouridine (mcm5s2U) Modification Utilizing the Gamma-Toxin Endonuclease            Jenna M. Lentini and Dragony Fu 14. Analysis of Queuosine tRNA Modifications Using APB Northern Blot Assays            Cansu Cirzi an

This volume discusses the latest experimental and clinical approaches to study seizures and epilepsy. Chapters in this book cover detailed protocols for ex vivo and in vitro experimental models and widely-used in vivo (acute and chronic seizure) models in epilepsy research.

Part I: Small Molecules 1. Measurement of Transcellular Transport Rates and Intracellular Drug Sequestration in the Presence of an Extracellular Concentration Gradient            Kyoung Ah Min and Gus R. Rosania 2. Kinetic Design for Establishing Long Term Stationary Cytosol Concentrations during Drug Transport across P-gp Expressing Confluent Cell Monolayers to Facilitate Measuring Cytosol Concentration, Fitting Drug Molar Partition Coefficients into the Cytosolic Monolayer of the Plasma Membrane and Kinetically Identifying Drug Uptake Transporters            Joe Bentz 3. In Vitro Methodologies to Assess Potential for Transporter-Mediated Drug-Drug Interactions            Jibin Li, Qing Wang, and Ismael J. Hidalgo 4. Determination of Fraction Unbound and Unbound Partition Coefficient to Estimate Intracellular Free Drug Concentration            Sangwoo Ryu, Keith Riccardi, Samantha Jordan, Nathaniel Johnson, and Li Di 5. Quantitative Analysis of Intracellular Drug Concentrations in Hepatocytes            Chitra Saran, James J. Beaudoin, Nathan D. Pfeifer, and Kim L.R. Brouwer 6. Quantification of Intracellular Drug Aggregates and Precipitates            Phillip Rzeczycki and Gus R. Rosania 7. Quantitative Phenotypic Analysis of Drug Sequestering Macrophage Subpopulations            Mikhail D. Murashov 8. Using an Integrated QSAR Model to Check Whether Small-Molecule Xenobiotics Will Accumulate in Biomembranes, with Particular Reference to Fluorescent Imaging Probes            Richard W. Horobin and Juan C. Stockert 9. Diversity-Oriented Fluorescence Library Approach (DOFLA) for Discovery of Cell-Permeable Probes for Applications in Live Cell Imaging            Dongdong Su and Young-Tae Chang Part II: Macromolecules, Biologics, and Nanoparticles 10. Overcoming Cellular and Systemic Barriers to Design the Next Wave of Peptide Therapeutics            Jerome Hochman, Tomi Sawyer, and Ruchia Duggal 11. Intracellular Targeting of Cyclotides for Therapeutic Applications            Nicole Lawrence and David J. Craik 12. Cellular Trafficking of Monoclonal and Bispecific Antibodies            John J. Rhoden and Christopher M. Wiethoff 13. Quantitative Drug Target Imaging Using Paired-Agent Principles            Kenneth M. Tichauer, Negar Sadeghipour, Yu "Winston" Wang, Summer L. Gibbs, Jonathan T.C. Liu, and Kimberley S. Samkoe 14. Quantitative Determination of Intracellular Bond Cleavage            Joshua A. Walker, Michelle R. Sorkin, and Christopher A. Alabi 15. Development and Application of a Single Cell-Level PK-PD Model for ADCs 

1. Isolation of Lipid Rafts by the Detergent and Non-Detergent Based Methods for Localization of GPCRs with Immunoblotting and Laser Scanning Confocal Microscopy            Peter Abdelmaseeh, Andrew C. Tiu, Selim Rozyyev, Laureano D. Asico, Pedro A. Jose, Van Anthony M. Villar 2. Detection of GPCR mRNA Expression in Primary Cells via qPCR, Microarrays, and RNA-Sequencing            Krishna Sriram, Cristina Salmer├│n, Anna Di Nardo, and Paul A. Insel 3. Construction of Recombinant Cell Lines for GPCR Expression            Philip J. Reeves 4. Recombinant Expression and Purification of Cannabinoid Receptor CB2, a G Protein-Coupled Receptor            Alexei A. Yeliseev 5. Screening for Serotonin Receptor 4 Agonists Using GPCR-Based Sensor in Yeast            Emily A. Yasi and Pamela Peralta-Yahya 6. Immobilization of Olfactory Receptors Carried by Nanosomes onto a Gold Sensor Surface            Jasmina Vidic and Yanxia Hou 7. Screening Methods for Cell-Free Synthesized GPCR/Nanoparticle Samples            Zoe K├╢ck, Volker D├╢tsch, and Frank Bernhard 8. Fluorescence Anisotropy-Based Assay for Characterization of Ligand Binding Dynamics to GPCRs: The Case of Cy3B-Labelled Ligands Binding to MC4 Receptors in Budded Baculoviruses            Santa Veiksina, Maris-Johanna Tahk, T├╡nis Laasfeld, Reet Link, Sergei Kopanchuk, and Ago Rinken 9. Bioluminescence in G Protein-Coupled Receptors Drug Screening Using Nanoluciferase and Halo-Tag Technology            Hannes Schihada, Katarina Nemec, Martin J. Lohse, and Isabella Maiellaro 10. Nanoluciferase-Based Complementation Assay to Detect GPCR-G Protein Interaction            C├⌐line Laschet and Julien Hanson 11. Imaging of Genetically-Encoded FRET-Based Biosensors to Detect GPCR Activity            Luca Bordes, Sergei Chavez-Abiega, and Joachim Goedhart 12. cAMP Biosensor Assay Using BacMam Expression System: Studying the Downstream Signaling of LH/hCG Receptor Activation            Darja Lavogina, T├╡nis Laasfeld, Maris-Johanna Tahk, Olga Kukk, Anni Allikalt, Sergei Kopanchuk, and Ago Rinken 13. FLIPR Calcium Mobilization Assays in GPCR Drug Discovery            Grzegorz Woszczek, Elisabeth Fuerst, and Thomas J.A. Maguire 14. Live Cell Imaging and Optogenetics-Based Assays for GPCR Activity            Xenia Meshik and N. Gautam 15. Split-Tobacco Etch Virus (Split-TEV) Method in G Protein-Coupled Receptor Interacting Proteins            Marta Alonso-Gard├│n and Ra├║l Est├⌐vez 16. NanoLuc-Based Methods to Measure ╬▓-Arrestin2 Recruitment to G Protein-Coupled

The aim of this book is to describe the underlying principles of algebraic geometry, some of its important developments in the twentieth century, and some of the problems that occupy its practitioners today. It is intended for the working or the aspiring mathematician who is unfamiliar with algebraic geometry but wishes to gain an appreciation of its foundations and its goals with a minimum of prerequisites. Few algebraic prerequisites are presumed beyond a basic course in linear algebra.

This second edition describes up-to-date methodological approaches, ranging from physiological assays to imaging and molecular techniques, to study a wide variety of plant responses to environmental cues. Chapters are divided into four sections detailing protocols to investigate key biological processes underlying plant environmental responses in the model organisms Arabidopsis thaliana and Physcomitrella patens as well as in different crop species. 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, Environmental Responses in Plants, Second Edition aims to be a foundation for future studies and to be a source of inspirationfor new investigations in the field.

This volume provides protocols and methods on techniques to study plant gametogenesis. Chapters are divided into four sections covering omics, cytological, molecular approaches, plant transformation, genome editing, bioinformatics, and data analysis. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Plant Gametogenesis: 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 volume provides an updated collection of protocols for manipulating and studying VEGF signaling pathways in vitro and in vivo and aims to present a range of both firmly established and newly emerging technologies. Covering multiple model species, from mouse to zebrafish to human, the book explores the role of VEGF and VEGFR isoforms in exosomes, cultured cells, or in tissues, as well as robust cell assays for the investigation of basic angiogenic mechanisms and VEGF signaling in more complex cellular systems, amongst other subjects. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, VEGF Signaling: Methods and Protocols, Second Edition provides a useful tool for researchers in the vascular biology community and beyond in understanding the basic biology of VEGF signaling and in translating this research into the clinic.

This volume provides cutting-edge techniques to further the study chromatin biology. Chapters include both novel and well-established methods for the analysis of DNA-associated proteins, DNA methylation, three-dimensional chromatin interactions, deep sequencing-based tools, and data analysis pipelines. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, provides details of the necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and describes step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Chromatin: Methods and Protocols aims to further the understanding of how modified DNA and associated proteins affect the transcriptional output of the genome.Chapter Genome-wide mapping and microscopy visualization of protein-DNA interactions by pA-DamID [Chapter 12] is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

This volume contains a comprehensive collection of laboratory protocols used by researchers to analyze varied aspects of non-alcoholic steatohepatitis (NASH). The chapters in this book cover topics such as methods for histological diagnosis of NASH; the purpose of generating an in vivo NASH model; protocols for isolating hepatocytes and Kupffer cells, bone marrow derived macrophages, and adipocytes; techniques to develop human pluripotent stem cells-derived liver organoids; single-cell and RNA-sequencing; and a description of how to extract exosomes and exosomal miRNAs from mesenchymal 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. Thorough and practical, Non-Alcoholic Steatohepatitis: Methods and Protocols is a valuable resource for new and experiences investigators studying NASH, and serves as an essential reference on NASH for basic and clinical researchers and students.

This volume provides both experienced and new microscopists with methods and protocols to perform fluorescence microscopy-based experiments. The book is divided into four parts detailing basic fluorescent microscopy, quantitative methods, imaging living animals, human tissue samples, approaches for imaging at a near-molecular level, and approaches to image analysis. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Fluorescent Microscopy aims to be a useful practical guide to researches to help further their study in this field.

This volume explores a collection of different protocols for the analysis and characterization of DNAzymes and their functions. The topics covered in this book range from bioinformatics and molecular dynamics simulations for the study or modification of nucleic acids to the descriptions of spectroscopic, fluorescence-based, or crystallographic methods to understand the structure and function of DNAzymes. 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, DNAzymes: Methods and Protocols is a valuable resource for scientists and researchers interested in learning more about this evolving field.

This volume explores the latest techniques in inner ear development, analysis of its sensory cells, and characterization and manipulation of the central auditory and vestibular pathways. The chapters in this book cover topics such as dissection and imaging of the cochlea; behavioral evaluation of animal models of diseases like tinnitus; hair cell function and regeneration; and recent advances in sequencing technology. 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 comprehensive, Developmental, Physiological, and Function Neurobiology of the Inner Ear is a valuable resource for scientists and researchers interested in learning more about this developing field.

This open access volume gathers a variety of models, delivery systems, and approaches that can be used to assess RNA technology for exploiting antisense as a therapeutic intervention. Beginning with a section on the design of antisense technology and their delivery, the book continues by covering model systems developed to evaluate efficacy, both in vivo and in vitro, as well as methods to evaluate preclinically the toxicity associated with these new potential drugs, and intellectual property considerations. 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, Antisense RNA Design, Delivery, and Analysis provides basic knowledge and a large collection of methods to facilitate the work of newcomers to this vibrant and expanding field. This book was conceived thanks to the network DARTER (Delivery of Antisense RNA Therapeutics). DARTER is funded by the EU Cooperation of Science and Technology (COST), which aims to enhance interaction and collaborations between researchers in Europe and other countries.

This detailed volume explores perspectives and methods using cell-free expression (CFE) to enable next-generation synthetic biology applications. The first section focuses on tools for CFE systems, including a primer on DNA handling and reproducibility, as well as methods for cell extract preparation from diverse organisms and enabling high-throughput cell-free experimentation. The second section provides an array of applications for CFE systems, such as metabolic engineering, membrane-based and encapsulated CFE, cell-free sensing and detection, and educational kits. 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, Cell¿Free Gene Expression: Methods and Protocols serves as an ideal guide for researchers seeking technical methods to current aspects of CFE and related applications.

This volume provides an up-to-date collection of protocols describing some of the key methods to investigate the integrated stress response (ISR), a vital evolutionarily conserved mechanism that enables eukaryotic cells to adapt to stress conditions and alter their gene expression programs. The content of the book is split between techniques to analyze mRNA translation regulation and methods to analyze interaction networks and ribonucleoprotein (RNP) granules. 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, The Integrated Stress Response: Methods and Protocols serves as an ideal guide to help accelerate research into the complex and fascinating biology of the ISR.

This fully updated book explores all-new and revised protocols involving the use of in silico models, particularly with regard to pharmaceuticals. Divided into five sections, the volume covers the modeling of pharmaceuticals in the body, toxicity data for modeling purposes, in silico models for multiple endpoints, a number of platforms for evaluating pharmaceuticals, as well as an exploration of challenges, both scientific and sociological. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and implementation advice necessary for successful results. Authoritative and comprehensive, In Silico Methods for Predicting Drug Toxicity, Second Edition aims to guide the reader through the correct procedures needed to harness in silico models, a field which now touches a wide variety of research specialties.

This volume provides detailed, up-to-date methods used in research on Atherosclerosis. Chapters guide readers through an overview of the pathogenesis of atherosclerosis and model systems together with in vitro, ex vivo, in vivo and emerging methods in atherosclerosis research. 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, Atherosclerosis: Methods and Protocols serves as an invaluable resource for those engaging in research on atherosclerosis and cardiovascular disease, as well as for researchers who are new to the field and students at both the undergraduate and postgraduate level.

This volume details methods and protocols covering multiple aspects of Medulloblastoma. Divided into four parts, chapters guide readers through nucleic acids detection and analysis, cell-based analysis methodologies, and applications of patient-information on designing better experimental strategies for future drug development efforts in Medulloblastoma. 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, Medulloblastoma: Methods and Protocols aims to deliver a clear-cut and standardized set of protocols to a broad scientific community.