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• 1. Introduction to Laboratory Practices
• 2. Dos and Don'ts in the Lab
• 3. Equipment Care
• 4. Agarose Gel Electrophoresis
• 5. SDS-PAGE
• 6. DNA plasmid isolation using Alkaline Lysis Method from E.coli DH5 cells
• 7. Restriction digestion of Plasmid DNA
• 8. Genomic DNA extraction from plant leaves using CTAB method
• 9. Genomic DNA extraction from Silk Worm using modified phenol: chloroform method (Suzuki et al., 1972)
• 10. Genomic DNA extraction from Fungal Mycelium using modified Cenis, 1992 method
• 11. Bacterial transformation protocol using CaCl2
• 12. Centrifugation- Principle and Types
• 13. Various Chromatographic techniques
• 14. Thin Layer Chromatography
• 15. Gel Filtration/Size Exclusion Chromatography
• 16. Ion Exchange Chromatography
• 17. Affinity Chromatography
• 18. Paper Chromatography
• 19. Growth of bacterial cultures and preparation of growth curve
• 20. Polymerase Chain Reaction
• 21. Blotting/ Hybridization
• 22. Dot Blot Analysis
• 23. ELISA
• 24. Standard Operating Procedures (SOPs) for various equipment.
• (source: Nielsen Book Data)

Advanced Methods in Molecular Biology and Biotechnology: A Practical Lab Manual is a concise reference on common protocols and techniques for advanced molecular biology and biotechnology experimentation. Each chapter focuses on a different method, providing an overview before delving deeper into the procedure in a step-by-step approach. Techniques covered include genomic DNA extraction using cetyl trimethylammonium bromide (CTAB) and chloroform extraction, chromatographic techniques, ELISA, hybridization, gel electrophoresis, dot blot analysis and methods for studying polymerase chain reactions. Laboratory protocols and standard operating procedures for key equipment are also discussed, providing an instructive overview for lab work. This practical guide focuses on the latest advances and innovations in methods for molecular biology and biotechnology investigation, helping researchers and practitioners enhance and advance their own methodologies and take their work to the next level.
(source: Nielsen Book Data)

• Allostery: The Rebound of Proteins
• Disclosing Allostery Through Protein Contact Networks
• Identification of Allosteric Effects in Proteins by Elastic Network Models
• Locating and Navigating Energy Transport Networks in Proteins
• Probing Allosteric Mechanism with Long-Range Rigidity Transmission across Protein Networks
• Protein Assembly: Defining the Strength of Protein-Protein Interactions Coupling the Theory with Experiments
• Network Re-Wiring during Allostery and Protein-Protein Interactions: A Graph Spectral Approach
• Topology Results on Adjacent Amino Acid Networks of Oligomeric Proteins
• Community Network Analysis of Allosteric Proteins
• The PyInteraph Workflow for the Study of Interaction Networks Form Protein Structural Ensembles
• The Allosteric Effect in Antibody-Antigen Recognition
• Distal Regions Regulate Dihydrofolate Reductase-Ligand Interactions
• Investigating Conformational Dynamics and Allostery in the p53 DNA-Binding Domain Using Molecular Simulations
• Molecular Dynamics Simulation Techniques as a Tool in Drug Discovery and Pharmacology: A Focus on Allosteric Drugs
• Cooperativity and Allostery in RNA Systems.

This volume explores the basic issues of allostery and network that are fundamental to studying this field. Chapters in this book look at how the basic machine-like proteins, that are similar to human machines, need to be organized, architecturally, to relate to different organizational layers. Chapters cover topics such as methodological/computational factors focused on links between allostery and network formalism; the presence of oscillating modes transversing the structure and underlying network wiring of the allosteric process; the action at distance by transduction of signals across an organized network structure; and the P53 protein located at the cross-road of cell cycle regulation, genome integrity, and cancer development. 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, Allostery: Methods and Protocols is a valuable resource for any scientists and researcher interested in learning more about this developing field.

• Series Preface... Preface... Foreword... Table of Contents... Contributing Authors...
• 1. Highly Processed Food and Binge Eating Ashley Gearhardt
• 2. The Binge Eating Prone/Binge Eating Resistant Animal Model: A Valuable Tool for Examining Neurobiological Underpinnings of Binge Eating Natasha Fowler, Nicollette Russell, Cheryl L. Sisk, Alexander W. Johnson, and Kelly L. Klump
• 3. Food Seeking in Spite of Harmful Consequences Rossella Ventura, Lucy Babicola, Diego Andolina, Enrico Patrono, and Matteo Di Segni
• 4. Assessment of Binge-Like Eating Behavior in Mice Utilizing a Weekly Intermittent Access Paradigm Tiffany Tang, Natalie Barker, James Krantz, Alysia Polito, Petr Telensky, Michael A. Statnick, and Traci Czyzyk
• 5. Predicting and Classifying Rats Prone to Overeating Fat Jessica R. Barson, Irene Morganstern, and Sarah F. Leibowitz
• 6. Psychosocial Stress and Diet History Promote Emotional Feeding in Female Rhesus Monkeys Vasiliki Michopoulos, Kelly Ethun, and Mark E. Wilson
• 7. Artificial Sweeteners in Animal Models of Binge Eating Gaelle Awad, Katia Befort, and Mary C. Olmstead
• 8. Intermittent, Extended Access Rodent Models of Compulsive Eating Eric P. Zorrilla, Alison D. Kreisler, and Samantha R. Spierling
• 9. Animal Models of Binge Eating: Hedonic Feeding and Alcohol Intake Julianna N. Brutman, Sunil Sirohi, and Jon F. Davis
• 10. Animal Models of Binge Eating Palatable Foods: Emergence of Addiction-Like Behaviors and Brain Changes in the Rat Miriam E. Bocarsly and Nicole M. Avena
• 11. Clinical and Preclinical Bariatric Surgery Approaches to Studying Obesity Panayotis K. Thanos, Abdulraouf Lamoshi, Amanda Nubelo, John Hamilton, Artur Chernoguz, Aaron B. Hoffman, Teresa Quattrin, and Carroll Harmon
• 12. Preference for Palatable Food, Impulsivity, and Relation to Drug Addiction in Rats Marilyn E. Carroll, Natalie E. Zlebnick, and Nathan A. Holtz
• 13. Impact of a History of Caloric Restriction and a Frustration Stress Manipulation on Binge-Like Eating Behavior in Female Rats: Preclinical Results Maria Vittoria Micioni Di Bonaventura, Emanuela Micioni Di Bonaventura, Luca Botticelli, and Carlo Cifani
• 14. Anorexia and Undereating Guido K.W. Frank
• 15. Activity-Based Anorexia, An Animal Model of Anorexia Nervosa for Investigating Brain Plasticity Underlying the Gain of Resilience Chiye Aoki
• 16. The Anorectic Phenotype of the anx/anx Mouse is Associated with Hypothalamic Dysfunction Ida A.K. Nilsson, Tomas Hoekfelt, and Martin Schalling
• 17. Exploring the Neural Underpinnings of an Antidepressant and Rewarding Action of Early Anorexia Valerie Compan
• 18. Food-Anticipatory Activity: Rat Models and Underlying Mechanisms Roger A.H. Adan
• 19. In Search for Perfection: An Activity-Based Rodent Model of Anorexia Magdalena Kurnik-Lucka, Kamil Skowron, and Krzysztof Gil Subject Index List...
• (source: Nielsen Book Data)

This second edition volume expands on the previous edition with discussions on the latest techniques and animal models used to study eating disorders, and the characterizations of behaviors and neurochemical alterations associated with them. Chapters in this book cover different contributing factors of eating disorders and explore topics such as highlight processed food and binge eating; predicting and classifying rates prone to overeating fat; artificial sweeteners in animal models of binge eating; clinical and preclinical bariatric surgery approaches to studying obesity; anorexia and undereating; and food-anticipatory activity in rat models and its underlying mechanisms. 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, Animal Models of Eating Disorders, Second Edition is a valuable resource for any researchers interested in learning more about this important and developing field. .
(source: Nielsen Book Data)

• Handling Arabidopsis and other Brassicaceae: Growth, Preservation of Seeds, Transformation and Genetic Crosses
• Bioinformatic Tools in Arabidopsis Research
• Analyses of Natural Variation: Field Experiments and Nucleotide Diversity for Your Favorite Gene
• Non-sterile Grafting Methods for Arabidopsis
• CRISPR/Cas9-based Genome Editing Toolbox for Arabidopsis thaliana
• Transient Transformation of A. thaliana Seedlings by Vacuum Infiltration
• Transient Expression of Fluorescent Fusion Proteins in Arabidopsis Protoplasts
• Photosynthetic and Heterotrophic Cell Suspension Cultures
• Genome-wide Association Studies in Arabidopsis thaliana: Statistical Analysis and Network-Based Augmentation of Signals
• Visualising and Measuring Single Locus Dynamics in Arabidopsis thaliana
• Identification and Quantification of Small RNAs
• Flow Cytometry and Sorting in Arabidopsis
• Live Imaging of Arabidopsis Leaf and Vegetative Meristem Development
• Using Genetically Encoded Fluorescent Biosensors for Quantitative in vivo Imaging
• Using Tripartite Split-sfGFP for the Study of Membrane ProteinProtein Interactions
• High-pressure Freezing and Freeze Substitution for Transmission Electron Microscopy Imaging and Immunogold-labeling
• Atomic Force Microscopy to Study Cell Wall Mechanics in Plants
• Identification and Characterization of Reproductive Mutations in Arabidopsis
• Metabolomic Analysis of Natural Variation in Arabidopsis
• Untargeted Metabolomics of Arabidopsis Stomatal Immunity
• Biotin-based Proximity Labeling Of Protein Complexes in Planta
• Phosphoproteomic Analysis of Plant Membranes
• RNA-binding Protein Immunoprecipitation and High Throughput Sequencing. .

This fourth edition compiles the most recent methodologies developed to exploit the Arabidopsis genome. Chapters detail access to public resources, to genetic, cell biology, biochemical and physiological techniques, and sections on genome, transcriptome, proteome, metabolome and other whole-system approaches. 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, Arabidopsis Protocols, Fourth Edition aims to ensure successful results in the further study of this vital field.

• 1. Identifying Genotype-Phenotype Correlations via Integrative Mutation Analysis Edward Airey, Stephanie Portelli, Joicymara S. Xavier, YooChan Myung, Michael Silk, Malancha Karmakar, Joao P. L. Velloso, Carlos H. M. Rodrigues, Hardik H. Parate, Hardik H. Parate, Anjali Garg, Raghad Al-Jarf, Lucy Barr, Juliana A. Geraldo, Pamela M. Rezende, Douglas E.V. Pires, and David B. Ascher
• 2. Machine Learning for Biomedical Time Series Classification: From Shapelets to Deep Learning
• Christian Bock, Michael Moor, Catherine R. Jutzeler, and Karsten Borgwardt
• 3. Siamese Neural Networks: An Overview
• Davide Chicco
• 4. Computational Methods for Elucidating Gene Expression Regulation in Bacteria
• Kratika Naskulwar, Ruben Chevez-Guardado, and Lourdes Pena-Castillo
• 5. Neuro-evolutive Algorithms Applied for Modeling Some Biochemical Separation Processes
• Silvia Curteanu, Elena-Niculina Dragoi, Alexandra Cristina Blaga, Anca Irina Galaction, and Dan Cascaval
• 6. Computational Approaches for de novo Drug Design: Past, Present, and Future
• Xuhan Liu, Adriaan P. IJzerman, and Gerard J. P. van Westen
• 7. Data Integration Using Advances in Machine Learning in Drug Discovery and Molecular Biology Irene Lena Hudson
• 8. Building and Interpreting Artificial Neural Network Models for Biological Systems
• T. Murlidharan Nair
• 9. A Novel Computational Approach for Biomarker Detection for Gene Expression based Computer Aided Diagnostic Systems for Breast Cancer Ali Al-Yousef and Sandhya Samarasinghe
• 10. Applying Machine Learning for Integration of Multi-modal Genomics Data and Imaging Data to Quantify Heterogeneity in Tumour Tissues
• Xiao Tan, Andrew T Su, Hamideh Hajiabadi, Minh Tran, and Quan Nguyen
• 11. Leverage Large-scale Biological Networks to Decipher the Genetic Basis of Human Diseases Using Machine Learning
• Hao Wang, Jiaxin Yang, and Jianrong Wang
• 12. Predicting Host Phenotype based on Gut Microbiome using a Convolutional Neural Network Approach
• Derek Reiman, Ali M. Farhat, and Yang Dai
• 13. Predicting Hot-Spots using a Deep Neural Network Approach
• Antonio J. Preto, Pedro Matos-Filipe, Jose G. Almeida, Joana Mourao, and Irina S. Moreira
• 14. Using Neural Networks for Relation Extraction from Biomedical Literature
• Diana Sousa, Andre Lamurias, and Francisco M. Couto
• 15. A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models
• Eshel Faraggi, Robert L. Jernigan, and Andrzej Kloczkowski
• 16. Secure and Scalable Collection of Biomedical Data for Machine Learning Applications
• Charles Fracchia
• 17. AI-based Methods and Technologies to Develop Wearable Devices for Prosthetics and Predictions of Degenerative Diseases
• Mario Malcangi .
• (source: Nielsen Book Data)

This volume presents examples of how Artificial Neural Networks (ANNs) are applied in biological sciences and related areas. Chapters cover a wide variety of topics, including the analysis of intracellular sorting information, prediction of the behavior of bacterial communities, biometric authentication, studies of Tuberculosis, gene signatures in breast cancer classification, the use of mass spectrometry in metabolite identification, visual navigation, and computer diagnosis. 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, Artificial Neural Networks: Third Edition should be of value to all scientists interested in the hands-on application of ANNs in the biosciences.
(source: Nielsen Book Data)

Botany: A Lab Manual, Seventh Edition is mapped to match Botany: An Introduction to Plant Biology, Seventh Edition but is the perfect companion for any botany course. Packed with hands-on activities, it engages students and broadens their understanding of plant biology. Now in full color and a convenient lay-flat format, it provides detailed examination of plant structure, plant groups, genetics, classification, and more. Featuring additional case studies and image labeling activities, Botany: A Lab Manual is the clear choice for students digging into this exciting science.
(source: Nielsen Book Data)

• Part I: Cancer Resistance
• 1. Fighting Cancer Resistance: An Overview
• Martha Robles-Flores
• 2. Prostate Cancer Spheroids: A Three-Dimensional Model for Studying Tumor Heterogeneity
• Mauricio Rodriguez-Dorantes, Carlos David Cruz-Hernandez, Sergio Alberto Cortes-Ramirez, Jenie Marian Cruz-Burgos, Juan Pablo Reyes-Grajeda, Oscar Peralta-Zaragoza, and Alberto Losada-Garcia
• 3. Enrichment and Transcriptional Characterization of Stem Cells Isolated from Human Glioblastoma Cell Lines
• Ana G. Pina-Medina, Ana M. Hernandez-Vega, Nestor F. Diaz, Ismael Mancilla-Herrera, and Ignacio Camacho-Arroyo
• 4. Reverse Docking for the Identification of Molecular Targets of Anticancer Compounds
• Angel Jonathan Ruiz-Moreno, Alexander Doemling, and Marco Antonio Velasco-Velazquez
• 5. Mouse Model for Efficient Simultaneous Targeting of Glycolysis, Glutaminolysis, and De Novo Synthesis of Fatty Acids in Colon Cancer
• Alejandro Schcolnik-Cabrera and Alfonso Duenas-Gonzalez
• Part II: Epigenetic Control of Cancer
• 6. Developing a Portable Device for the Identification of miRNAs in Fluids
• Alexander Asanov, Alicia Sampieri, and Luis Vaca
• 7. Methods for the Study of Long Non-Coding RNA in Cancer Cell Signaling
• Yi Feng, Junjie Jiang, Zhongyi Hu, Jiao Yuan, Tianli Zhang, Yutian Pan, Mu Xu, Chunsheng Li, Youyou Zhang, Lin Zhang, and Xiaowen Hu
• 8. RNA-Sequencing Analysis Pipeline for Prognostic Marker Identification in Cancer
• Sudhanshu Shukla and Seema Khadirnaikar
• Part III: Metastasis Promotion
• 9. Correlation of Circulating Tumor Cell Measurements with 3D Quantitative Tumor Characterization to Predict Clinical Outcomes in Cancer
• Sweet Ping Ng, Clifton David Fuller, and Heath Devin Skinner
• 10. Extracellular Vesicles and Their Roles in Cancer Progression
• Wen-Hsuan Chang, Richard A. Cerione, and Marc A. Antonyak
• 11. Analysis of Tumor-Derived Exosomes by Nanoscale Flow Cytometry
• Cynthia Lopez-Pacheco, Andrea Bedoya-Lopez, Roxana Olguin-Alor, and Gloria Soldevila
• 12. In Vitro Models for Studying Tumor Progression
• Juan Carlos Gonzalez-Orozco, Saul Gaona-Dominguez, and Ignacio Camacho-Arroyo
• 13. Assessment of Cell Cycle in Primitive Chronic Myeloid Leukemia Cells by Flow Cytometry after Co-Culture with Endothelial Cells
• Patricia Torres-Barrera, Mireya Ramirez-Florencio, and Antonieta Chavez-Gonzalez
• Part IV: New Technologies in the Study of Cancer
• 14. Chimeric Antigen Receptor (CAR) T-Cell Therapy for Cancer: Challenges and Opportunities
• Arimelek Cortes-Hernandez, Evelyn Alvarez-Salazar, and Gloria Soldevila
• 15. Cell-Internalization SELEX of RNA Aptamers as a Starting Point for Prostate Cancer Research
• Mauricio Rodriguez-Dorantes, Sergio Alberto Cortes-Ramirez, Jenie Marian Cruz-Burgos, Juan Pablo Reyes-Grajeda, Alberto Losada-Garcia, Vanessa Gonzalez-Covarrubias, and Carlos David Cruz-Hernandez
• 16. Generation of Functional Genetic Study Models in Zebrafish Using CRISPR-Cas9
• Francisco Carmona-Aldana, Hober N Nunez-Martinez, Carlos A Peralta-Alvarez, Gustavo Tapia-Urzua, and Felix Recillas-Targa
• 17. Developing a Model for a siRNA Delivery System by Cancer Implantation into Zebrafish Circulation
• Yasuhito Shimada and Mai Hazekawa
• 18. Fabrication of Adhesive Substrate for Incorporating Hydrogels to Investigate the Influence of Stiffness on Cancer Cell Behavior
• Genaro Vazquez-Victorio, Adriana Rodriguez-Hernandez, Mariel Cano-Jorge, Ana Ximena Monroy-Romero, Marina Macias-Silva, and Mathieu Hautefeuille.
• (source: Nielsen Book Data)

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. Beginning with an important section on cancer resistance, the main obstacle to effective cancer therapy, the book continues with chapters exploring state-of-the-art methods in epigenetic control of cancer, metastasis promotion, as well as a variety of new technologies in the study of cancer. 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 timely, Cancer Cell Signaling: Methods and Protocols, Third Edition serves as an ideal guide to researchers seeking to overcome the challenges in the vital field of cancer cell signaling.
(source: Nielsen Book Data)

• Part I: Basic Science
• 1. Molecular Dynamics Simulations of Channelrhodopsin Chimera, C1C2
• Monika R. VanGordon
• 2. Computing Potential of the Mean Force Profiles for Ion Permeation through Channelrhodopsin Chimera, C1C2
• Chad Priest, Monika R. VanGordon, Caroline Rempe, Mangesh Chaudhari, Mark Stevens, Steve Rick, and Susan B. Rempe
• 3. Nanodisc Reconstitution of Channelrhodopsins Heterologously Expressed in Pichia pastoris for Biophysical Investigations
• Maria Walter and Ramona Schlesinger
• 4. Characterizing Channelrhodopsin Channel Properties via Two-Electrode Voltage Clamp and Kinetic Modeling
• Lindsey Prignano, Lauren Herchenroder, and Robert E. Dempski
• Part II: Cells
• 5. Charge Transport by Light-Activated Rhodopsins Determined by Electrophysiological Recordings
• Tamara Hussein and Christian Bamann
• 6. Probing Channelrhodopsin Electrical Activity in Algal Cell Populations
• Oleg A. Sineshchekov, Elena G. Govorunova, and John L. Spudich
• 7. Two-Photon Optogenetic Stimulation of Drosophila Neurons
• Mehmet Fisek and James M. Jeanne
• 8. Probing Synaptic Signaling with Optogenetic Stimulation and Genetically-Encoded Calcium Reporters
• Gabriel B. Borja, Himali Shroff, Hansini Upadhyay, Pin W. Liu, Valeriya Baru, Yung-Chih Cheng, Owen B. McManus, Luis A. Williams, Graham T. Dempsey, and Christopher A. Werley
• 9. Optogenetics to Interrogate Neuron-Glia Interactions in Pups and Adults
• Chloe Habermacher, Blandine Manot-Saillet, Domiziana Ortolani, Fernando C. Ortiz, and Maria Cecilia Angulo
• 10. Chronic Optogenetic Pacing of Human Induced Pluripotent Stem Cell-Derived Engineered Cardiac Tissues
• Marc Dwenger, William J. Kowalski, Hidetoshi Masumoto, Takeichiro Nakane, and Bradley B. Keller
• Part III: Animals
• 11. Patterned Optogenetic Stimulation Using a DMD-Projector
• Aanchal Bhatia, Sahil Moza, and Upinder S. Bhalla
• 12. Selecting Channelrhodopsin Constructs for Optimal Visual Restoration in Differing Light Conditions
• Tushar H. Ganjawala and Zhuo-Hua Pan
• 13. Recording Channelrhodopsin-Evoked Field Potentials and Startle Responses from Larval Zebrafish
• Yagmur Idil Ozdemir, Christina A. Hansen, Mohamed A. Ramy, Eileen L. Troconis, Lauren D. McNeil, and Josef G. Trapani
• 14. Automated Functional Screening for Modulators of Optogenetically-Activated Neural Responses in Living Organisms
• Ross C. Lagoy, Eric Larsen, and Dirk R. Albrecht
• 15. Optogenetic Interrogation of ChR2-Expressing GABAergic Interneurons after Transplantation into the Mouse Brain
• Muhammad N. Arshad, Gloster B. Aaron, and Janice R. Naegele
• 16. Application of Targeting-Optimized Chronos for Stimulation of the Auditory Pathway
• Antoine Huet and Vladan Rankovic
• 17. Channelrhodopsins for Cell-Type Specific Illumination of Cardiac Electrophysiology
• Marbely C. Fernandez, Ramona A. Kopton, Ana Simon Chica, Josef Madl, Ingo Hilgendorf, Callum M. Zgierski-Johnston, and Franziska Schneider-Warme
• 18. Optogenetic Control of Cardiac Autonomic Neurons in Transgenic Mice
• Angel Moreno, Grant Kowalik, David Mendelowitz, and Matthew W. Kay
• 19. Dissecting Mechanisms of Motivation within the Nucleus Accumbens Using Optogenetics
• Shannon L. Cole and Jeffrey J. Olney
• 20. Optogenetic Stimulation of the Central Amygdala Using Channelrhodopsin
• Anna S. Knes, Charlotte M. Freeland, and Mike J.F. Robinson
• 21. Optical Manipulation of Perfused Mouse Heart Expressing Channelrhodopsin-2 in Rhythm Control
• Xi Wang and Yue Cheng
• 22. Chronic Optogenetic Stimulation in Freely-Moving Rodents
• Thiago C. Moulin.
• (source: Nielsen Book Data)

This book merges approaches in understanding the function of the light-gated ion channels known as channelrhodopsin together with methods addressing how channelrhodopsins can be used to address biomedical questions on a cellular or organismal level. Since the first molecular identification of channelrhodopsins, a broad range of tools have been created and new approaches developed to both better understand the molecular determinants of channelrhodopsin function as well as to use these and homologous proteins from a variety of species as tools to better understand physiological processes, which this volume addresses. Additionally, channelrhodopsins have become instrumental as a potential treatment for disease states. 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, Channelrhodopsin: Methods and Protocols provides a resource for those interested in honing their current expertise in this vital area of study as well as potentially branching out into new directions.
(source: Nielsen Book Data)

• Isolation of Chondrocytes from Human Cartilage and Cultures in Monolayer and 3D
• Protocol for the Isolation of Intact Chondrons from Healthy and Osteoarthritic Human Articular Cartilage
• Cartilage-Specific Cre Recombinase Transgenes/Alleles in the Mouse
• Isolation of Mouse Growth Plate and Articular Chondrocytes for Primary Cultures
• Fetal Growth Plate Cartilage: Histological and Immunohistochemical Techniques
• Preparation of Adult Mouse Skeletal Tissue Sections for RNA In Situ Hybridization
• MicroRNA In Situ Hybridization in Paraffin-Embedded Human Articular Cartilage and Mouse Knee Joints
• Laser Capture Microdissection of Mouse Growth Plate Cartilage
• RNA Isolation from Articular Cartilage Tissue
• Small Nucleolar RNA Expression Profiling in Cartilage
• MicroRNA Expression Profiling, Target Identification, and Validation in Chondrocytes
• ChIP-Seq Assays from Mammalian Cartilage and Chondrocytes
• MicroRNAs and Regulation of Autophagy in Chondrocytes
• Mitochondrial Biogenesis, Activity, and DNA Isolation in Chondrocytes
• Assessing Chondrocyte Status by Immunofluorescence-Mediated Localization of Parkin Relative to Mitochondria.

This detailed book collects a variety of methods from investigators at the forefront of chondrocyte biology and pathology research that they have tailored for their research projects in order to tackle the unique properties and challenges of the chondrocyte and those of its tissue matrix. Divided into three parts, the volume explores experimental models to study chondrocytes, in vivo assays, as well as methods to characterize the chondrocyte phenotype with high-throughput or discrete assays on cells maintained in vivo, just isolated from their tissue (ex vivo), or cultured in vitro. Written in 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 cutting-edge, Chondrocytes: Methods and Protocols is an ideal guide for experts as well as newcomers in the cartilage field with the aim of sparking new research ideas in order to solve many of the pending mysteries regarding cartilage biology, disease mechanisms, and potential treatments.

• 1. Using a Design of Experiments Approach to Inform the Design of Hybrid Synthetic Yeast Promoters
• Computational Design of Multiplex Oligonucleotide-Based Assays
• Computational Methods For The Design Of Recombinase Logic Circuits
• Modular Modeling Of Genetic Circuits in SBML Level 3.-- CRISPR-ERA: A Webserver for Guide RNA Design of Gene Editing and Regulation
• iGUIDE Method for CRISPR Off-target Detection
• Web-based Base Editing Toolkits: BE-Designer and BE-Analyzer
• Synthetic Gene Circuit Analysis and Optimization
• Monitoring Single S. cerevisiae Cells with Multi-Frequency Electrical Impedance Spectroscopy in an Electrode-integrated Microfluidic Device
• Construction of Protein Expression Network
• Systems-theoretic Approaches to Design Biological Networks with Desired Functionalities
• A Deterministic Compartmental Modeling Framework for Disease Transmission
• Computer Aided Assembly and Verification of Synthetic Chromosomes
• Minimal Genome Design Algorithms using Whole-Cell Models
• Tn-Core: Functionally Interpreting Transposon-Sequencing Data with Metabolic Network Analysis
• Genome-scale Metabolic Modeling of Escherichia coli and its Chassis Design for Synthetic Biology Applications
• A Systems Bioinformatics Approach to Interconnect Biological Pathways. .

This second edition book provides complete coverage of the computational approaches currently used in Synthetic Biology. New chapters detail computational methods and algorithms for the design of bio-components, insight on CAD programs, analysis techniques, and distributed systems. 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, Computational Methods in Synthetic Biology, Second Edition aims to feature a broad overview of the research areas that can be met in the area of in silico Synthetic Biology.

• 1. Biomimetic Boundary-based Scaffold Design for Tissue Engineering Applications
• Henrique A. Almeida and Paulo J. Bartolo
• 2. Triply Periodic Minimal Surfaces (TPMS) for the Generation of Porous Architectures Using Stereolithography
• Sebastien B.G. Blanquer
• 3. 3D Printing Of Functionally-graded Films by Controlling Process Parameters
• A. Bonfanti, L. Domenicale, and A. Bhaskar
• 4. Photocurable Biopolymers for Coaxial Bioprinting
• Marco Costantini, Andrea Barbetta, Wojciech Swieszkowski, Dror Seliktar, Cesare Gargioli, and Alberto Rainer
• 5. Synthesis of an UV-curable Divinyl-fumarate Poly- -Caprolactone for Stereolithography Applications
• Ronca A., Ronca S., Forte G., and Ambrosio L.
• 6. Nanocomposite Clay-based Bioinks for Skeletal Tissue Engineering
• Gianluca Cidonio, Michael Glinka, Yang-Hee Kim, Jonathan I. Dawson, and Richard O.C. Oreffo
• 7. Additive Manufacturing using Melt Extruded Thermoplastics for Tissue Engineering
• Andrea Roberto Calore, Ravi Sinha, Jules Harings, Katrien V. Bernaerts, Carlos Mota, and Lorenzo Moroni
• 8. Computer-aided Wet-spinning
• Dario Puppi and Federica Chiellini
• 9. Production of Scaffolds Using Melt Electrospinning Writing and Cell Seeding
• E. C. Bolle, D. Nicdao, P.D. Dalton, and T.R. Dargaville
• 10. Low Voltage Continuous Electrospinning: A Versatile Protocol for Patterning Nano-and Micro-Scared Fibers for Cell Interface
• Zhaoying Li, Xia Li, and Yan Yan Shery Huang
• 11. Direct Write Deposition of Thermogels
• Sara Maria Giannitelli, Valeria Chiono, and Pamela Mozetic
• 12. 3D Bioprinting of Complex, Cell-laden Alginate Constructs
• Atabak Ghanizadeh Tabriz, Dirk-Jan Cornelissen, and Wenmiao Shu
• 13. Surface Tension-assisted Additive Manufacturing of Tubular, Multicomponent Biomaterials
• Elia A. Guzzi, Heloise Ragelle, and Mark W. Tibbitt
• 14. Bioprinting of Complex Vascularized Tissues
• Wei Zhu, Claire Yu, Bingjie Sun, and Shaochen Chen
• 15. A Scaffold-free 3D Bioprinted Cartilage Model for in vitro Toxicology
• Pallab Datta, Yang Wu, Yin Yu, Kazim K. Moncal, and Ibrahim T. Ozbolat.
• (source: Nielsen Book Data)

This volume details protocols encompassing different aspects of computer aided design and manufacturing of 3D scaffolds and biofabricated constructs for tissue engineering applications. Chapters are divided into four parts covering optimization of scaffold architectures for computer aided tissue engineering, synthetic routes to biomaterials compatible, technological platforms and manufacturing processes, and relevant applicative scenarios. 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, Computer-Aided Tissue Engineering: Methods and Protocols aims to be useful for new and experienced laboratory researchers working on different aspects of corneal regeneration.
(source: Nielsen Book Data)

• Part I: In Silico Design and Optimization of Guide RNA Sequences
• 1. Cloud-Based Design of Short Guide RNA (sgRNA) Libraries for CRISPR Experiments
• Florian Heigwer and Michael Boutros
• 2. Web-Based CRISPR Toolkits: Cas-OFFinder, Cas-Designer, and Cas-Analyzer
• Gue-Ho Hwang, Jin-Soo Kim, and Sangsu Bae
• Part II: Chemically-Modified Guide RNAs
• 3. Chemical Modification of Guide RNAs for Improved CRISPR Activity in CD34+ Human Hematopoietic Stem and Progenitor Cells
• Jenny Shapiro, Adi Tovin, Ortal Iancu, Daniel Allen, and Ayal Hendel
• 4. Gene Disruption Using Chemically-Modified CRISPR-Cpf1 RNA
• Moira A. McMahon and Meghdad Rahdar
• 5. 'Split-and-Click' sgRNA
• Lapatrada Taemaitree, Arun Shivalingam, Afaf H. El-Sagheer, and Tom Brown
• 6. Chimeric DNA-RNA Guide RNA Designs
• Shuhan Lu, Ying Zhang, and Hao Yin
• Part III: Expanding the CRISPR Toolbox
• 7. Harnessing tRNA for Processing Ability and Promoter Activity
• David J.H.F. Knapp and Tudor A. Fulga
• 8. Targeting Noncoding RNA Domains to Genomic Loci with CRISPR-Display: Guidelines for Designing, Building, and Testing sgRNA-ncRNA Expression Constructs
• David M. Shechner
• 9. Controlling the Activity of CRISPR Transcriptional Regulators with Inducible sgRNAs
• Quentin R.V. Ferry
• 10. Gene Manipulation Using Fusion Guide RNAs for Cas9 and Cas12a
• Ha Rim Shin, Jiyeon Kweon, and Yongsub Kim
• Part IV: Characterization of CRISPR Efficacy and Specificity
• 11. Methods for Measuring CRISPR/Cas9 DNA Cleavage in Cells
• Christopher R. Cromwell, Juan Jovel, and Basil P. Hubbard
• 12. In Vitro Assays for Comparing the Specificity of First- and Next-Generation CRISPR/Cas9 Systems
• Christopher R. Cromwell and Basil P. Hubbard
• 13. Profiling Genome-Wide Specificity of CRISPR-Cas9 Using Digenome-Seq
• Daesik Kim and Jin-Soo Kim
• 14. Detection of CRISPR/Cas9-Generated Off-Target Effect by Integration-Defective Lentiviral Vector
• Xiaoling Wang, Youjun Wu, and Jiing-Kuan Yee
• 15. Genome-Wide CRISPR Off-Target DNA Break Detection by the BLISS Method
• Roberto Ballarino, Britta A.M. Bouwman, and Nicola Crosetto.
• (source: Nielsen Book Data)

This detailed volume focuses on the CRISPR-associated guide RNA and how it can be designed, modified, and validated for a broad repertoire of purposes. 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. It concludes with methods for measuring off-target guide RNA activity. 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 protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and essential, CRISPR Guide RNA Design: Methods and Protocols provides a comprehensive pipeline for guide RNA design and aims to be an invaluable resource in applying this powerful technology to basic research and therapeutic applications.
(source: Nielsen Book Data)

• Determination of Caspase Activation by Western Blot
• Detection of Unfolded Protein Response by Polymerase Chain Reaction
• Subcellular Fractionation to Demonstrate Activation of Intrinsic Apoptotic Pathway
• A Triple-Parameter Based Laboratory Friendly Fluorescence Imaging to Identify Apoptosis in Live Cells
• Flow Cytometric Analyses of p53-mediated Cell Cycle Arrest and Apoptosis in Cancer Cells
• A Real-Time, Bioluminescent Apoptosis Assay
• Detection of Anoikis Using Cell Viability Dye and Quantitation of Caspase Activity
• Time and Dose Dependent Toxicity Studies in 3D Cultures Using a Luminescent Lactate Dehydrogenase Assay
• Visualization and Quantification of Neutrophil Extracellular Traps
• 2In Vitro Identification and Isolation of Human Neutrophil Extracellular Traps
• Induction and Detection of Necroptotic Cell Death in Mammalian Cell Culture
• Visualization of Necroptotic Cell Death through Transmission Electron Microscopy
• Methodology for Comprehensive Detection of Pyroptosis
• Determination and Quantitation of Cytotoxic T Cell-Mediated Cell Death
• Detection of Immunogenic Cell Death in Tumor Vaccination Mouse Model
• A Luminescent Assay to Quantify Cell Viability in Real Time
• Kinetic Measurement of Apoptosis and Immune Cell Killing Using Live-Cell Imaging and Analysis
• Two Plasmid-Based Systems for CRISPR/Cas9 Mediated Knockout of Target Genes
• Determining Cell Death Pathway and Regulation by Enrichment Analysis
• Transcription Factor Binding Site Identification and Enrichment Analysis.

This volume provides detailed protocols for the performance, analysis, and troubleshooting of in vitro and in vivo experiments related to programmed cell death. Chapters compile conventional techniques such as western blot and qPCR and state-of-the art transmission electron microscopy and real-time multiplexed imaging assays. 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 accessible, Detection of Cell Death Mechanisms: Methods and Protocols aims to ensure seamless execution of protocols on specific cell death type.

• 1. Laboratory Culture and Mutagenesis of Amphioxus (Branchiostoma floridae)
• Linda Z. Holland and Guang Li
• 2. Handling and Manipulation of Gametes and Embryos of the Annelidan Worm Pseudopotamilla occelata
• Ryusaku Deguchi and Takeshi Nakano
• 3. The Starfish Asterina pectinifera: Collection and Maintenance of Adults and Rearing and Metamorphosis of Larvae
• Naoyuki Murabe, Ei-ichi Okumura, Kazuyoshi Chiba, Enako Hosoda, Susumu Ikegami, and Takeo Kishimoto
• 4. Experimental Tools to Study Regeneration in the Sea Anemone Nematostella vectensis
• Aldine R. Amiel and Eric Roettinger
• 5. Staining and Tracking Methods for Studying Sponge Cell Dynamics
• Carole Borchiellini, Sandie M. Degnan, Emilie Le Goff, Caroline Rocher, Amelie Vernale, Stephen Baghdiguian, Nina Sejourne, Florent Marschal, Andre Le Bivic, Nelly Godefroy, Bernard M. Degnan, and Emmanuelle Renard
• 6. Microscopy Studies of Placozoans
• Carolyn L. Smith, Tatiana D. Mayorova, Christine A. Winters, Thomas S. Reese, Sally P. Leys, and Andreas Heyland
• 7. Identification of SH2 Domain-Mediated Protein Interactions that Operate at Fertilization in the Sea Star Patiria miniata
• Lauren Bates, Emily Wiseman, Jamie Kitson, and David J. Carroll
• 8. Marine Nemertean Worms for Immunoblotting Studies of Oocyte Aging
• Stephen A. Stricker
• 9. Recovery of Sea Star Egg Cell Surface Proteins Released at Fertilization
• Emily Wiseman, Lauren Bates, and David J. Carroll
• 10. Quantifying Cell Proliferation During Regeneration of Aquatic Worms
• Eduardo E. Zattara and B. Duygu OEzpolat
• 11. In Situ Hybridization Techniques in the Homoscleromorph Sponge Oscarella lobularis
• Laura Fierro-Constain, Caroline Rocher, Florent Marschal, Quentin Schenkelaars, Nina Sejourne, Carole Borchiellini, and Emmanuelle Renard
• 12. Methodology for Whole Mount and Fluorescent RNA In Situ Hybridization in Echinoderms: Single, Double, and Beyond
• Margherita Perillo, Periklis Paganos, Maxwell Spurrell, Maria I. Arnone, and Gary M. Wessel
• 13. Gene Editing in the Ascidian Phallusia mammillata and Tail Nerve Cord Formation
• Alex McDougall, Celine Hebras, Isa Gomes, and Remi Dumollard
• 14. Transcriptomic Analysis in the Sea Anemone Nematostella vectensis
• Jacob F. Warner and Eric Roettinger
• 15. RNA Interference on Regenerating Holothurian Gut Tissues
• Miosotis Alicea-Delgado, Samir A. Bello-Melo, and Jose E. Garcia-Arraras
• 16. ATAC-Seq for Assaying Chromatin Accessibility Protocol Using Echinoderm Embryos
• Marta Silvia Magri, Danila Voronov, Jovana Randelovic, Claudia Cuomo, Jose Luis Gomez-Skarmeta, and Maria I. Arnone
• 17. Usage of the Sea Urchin Hemicentrotus pulcherrimus Database, HpBase
• Sonoko Kinjo, Masato Kiyomoto, Takashi Yamamoto, Kazuho Ikeo, and Shunsuke Yaguchi
• 18. Functional Genomic Studies of Trichoplax adhaerens Neuronal Activity
• Julia Gauberg, Adriano Senatore, and Andreas Heyland
• 19. A Bioinformatics Tutorial for Comparative Development Genomics in Diverse Meiofauna
• Joseph L. Sevigny, Jon L. Norenburg, and Francesca Leasi.
• (source: Nielsen Book Data)

This detailed second edition presents a wide variety of marine invertebrate model systems, from cephalochordata to holothurians, along with novel experimental protocols for taking advantage of their unique properties. The techniques range from culturing the organisms to modifying their DNA. 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, Developmental Biology of the Sea Urchin and Other Marine Invertebrates: Methods and Protocols, Second Edition is an ideal guide for researchers working with these versatile organisms and for furthering our understanding of fundamental biological questions.
(source: Nielsen Book Data)

• Preface... Table of Contents... Contributing Authors...
• 1. Ex Vivo Culture for Preimplantation Mouse Embryo to Analyse Pluripotency Katia Boutourlinsky, Nicolas Allegre, and Claire Chazaud
• 2. Microfabricated Device for High Resolution Imaging of Preimplantation Embryos Sandrine Vandormael-Pournin, Emmanuel Frachon, Samy Gobaa, and Michel Cohen-Tannoudji
• 3. In Vitro Culture of Mouse Blastocyst to the Egg Cylinder Stage via Mural Trophectoderm Excision Hatice O. Ozguldez and Ivan Bedzhov
• 4. Spatially Organized Differentiation of Mouse Pluripotent Stem Cells on Micropatterned Surfaces Sophie M. Morgani and Anna-Katerina Hadjantonakis
• 5. Mouse Primordial Germ Cells: In Vitro Culture and Conversion to Pluripotent Stem Cell Lines Malgorzata Borkowska and Harry G. Leitch
• 6. Generation of Primordial Germ Cell-Like Cells in Small and Large Scales Wolfram H. Gruhn and Ufuk Gunesdogan
• 7. Genome-Scale CRISPR Screening for Regulators of Cell Fate Transitions Valentina Carlini, Kristjan H. Gretarsson, and Jamie A. Hackett
• 8. Somatic Reprogramming by Nuclear Transfer Vincent Brochard and Nathalie Beaujean
• 9. Targeted Transgenic Mice using CRISPR/Cas9 Technology Fatima El Marjou, Colin Jouhanneau, and Denis Krndija
• 10. Whole-Mount Immunofluorescence Staining of Early Mouse Embryos Frederick C. K. Wong
• 11. Investigating the Inner Cell Mass of the Mouse Blastocyst by Combined Immunofluorescence Staining and RNA Fluorescent In Situ Hybridization Maud Borensztein
• 12. Mapping of Chromosome Territories by 3D-Chromosome Painting during Early Mouse Development Katia Ancelin, Yusuke Miyanari, Olivier Leroy, Maria-Elena Torres-Padilla, and Edith Heard
• 13. Deciphering the Early Mouse Embryo Transcriptome by Low-Input RNA-seq Raquel Perez-Palacios, Patricia Fauque, Aurelie Teissandier, and Deborah Bourc'his
• 14. Studying DNA Methylation Genome-Wide by Bisulfite Sequencing from Low Amounts of DNA in Mammals Ambre Bender, Hala Al Adhami, Thomas Dahlet, and Michael Weber
• 15. Profiling DNA Methylation Genome-Wide in Single Cells Antonio Galvao and Gavin Kelsey
• 16. Tracking Histone Modifications in Embryos and Low Input Samples using Ultrasensitive STAR ChIP-seq Bingjie Zhang, Xu Peng, Feng Xu, and Wei Xie
• 17. Chromatin Profiling in Mouse Embryonic Germ Cells by CUT&RUN Srinivasa Abishek Prakash and Joan Barau
• 18. DamID to Map Genome-Protein Interactions in Pre-Implantation Mouse Embryos Mrinmoy Pal, Kim de Luca, Jop Kind, and Maria-Elena Torres-Padilla
• 19. Understanding Chromosome Structure during Early Mouse Development by Single-Cell Hi-C Analysis Noemie Ranisavljevic, Maud Borensztein, and Katia Ancelin
• 20. Bioinformatic Analysis of Single Cell Hi-C Data from Early Mouse Embryo Samuel Collombet, Yuvia A. Perez-Rico, Katia Ancelin, Nicolas Servant, and Edith Heard Subject Index List...
• (source: Nielsen Book Data)

This volume explores the latest techniques used to study and understand chromatin reprogramming in embryos and germ cells. Various culture systems are presented, which consist of invaluable tools to investigate many developmental processes. This book also looks at methods for direct examination of DNA, RNA, and proteins in embryos, along with low-input and single-cell assays for exploring these features at the genome-wide scale. 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, Epigenetics Reprogramming During Mouse Embryogenesis: Methods and Protocols is a valuable resource for any scientist and researcher looking to make new discoveries in this fascinating field of chromatin reprogramming. .
(source: Nielsen Book Data)

• Germline Variation and Somatic Alterations in Ewing Sarcoma
• Western Blot Analysis in Ewing Sarcoma
• Tissue Preservation and FFPE Samples: Optimized Nucleic Acids Isolation in Ewing Sarcoma
• Liquid Biopsies in Ewing Sarcoma
• (Immuno-)histological Analysis of Ewing Sarcoma
• Molecular Approaches to Diagnosis In Ewing Sarcoma: Fluorescence in situ hybridization (FISH)
• Molecular Approaches to Diagnosis in Ewing Sarcoma: RT-PCR
• Molecular Approaches to Diagnosis in Ewing Sarcoma: Targeted RNA Sequencing
• Ewing-specific (re)expression Models
• Analysis of Regulatory Sequences by Dual-luciferase Reporter Assays in Ewing Sarcoma
• Proliferation Assessment by Trypan Blue Exclusion in Ewing Sarcoma
• Drug Screening by Resazurin Colorimetry in Ewing Sarcoma
• Analysis of Migration and Invasion in Ewing Sarcoma
• Genetically Engineered Mouse Model in Ewing Sarcoma
• Tumor Growth Analysis of Ewing Sarcoma Cell Lines Using Subcutaneous Xenografts in Mice
• Metastasis Assessment in Ewing Sarcoma Using Orthotopic Xenografts
• Orthotopic Implants in Mice
• Ewing Sarcoma PDX Models
• Using Zebrafish Larvae as a Xenotransplantation Model to Study Ewing Sarcoma
• Main Repositories and Databases used in Ewing Sarcoma Research
• Chromatin Immunoprecipitation Followed by Next-Generation Sequencing (ChIP-seq) Analysis in Ewing Sarcoma
• Epigenetic Analysis in Ewing Sarcoma
• Systems Biology Analysis for Ewing Sarcoma.

This volume aims at providing a selection of the most effective and widely employed protocols used in the Ewing sarcoma field. Chapters are divided into five sections detailing the molecular biology techniques used to analyze Ewing sarcoma including tissue preservation and methods used in morpho-molecular diagnostics and routine immune-histological analysis. Additional wet-lab protocols comprise in vitro techniques including re-expression and functional analyses of target genes together with in vivo tools and models such as patient-derived xenografts (PDX) and orthotopic xenografts for metastasis assessment in Ewing sarcoma. A full section on bioinformatic approaches to Ewing sarcoma covering ChIPseq, epigenetic and systems biology analyses finalizes this volume. 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 clearly written, Ewing sarcoma: Methods and Protocols aims to provide methods to further the study of Ewing sarcoma and bring researchers one step forward in the quest to fight this devastating disease.

• Bioinformatics Approaches for Functional Prediction of Long Non-Coding RNAs
• Visualization of lncRNA and mRNA Structure Models within the Integrative Genomics Viewer
• RNA Coding Potential Prediction Using Alignment-Free Logistic Regression Model
• Classification of Long Non-Coding RNAs by K-mer Content
• Genome-Wide Computational Analysis and Validation of Potential Long Non-Coding RNA-Mediated DNA-DNA:RNA Triplexes in the Human Genome
• Using INFERNO to Infer the Molecular Mechanisms Underlying Non-Coding Genetic Associations
• A Bioinformatic Pipeline to Integrate GWAS and eQTL Datasets to Identify Disease Relevant Human Long Non-Coding RNAs
• AnnoLnc: A One-Stop Portal to Systematically Annotate Novel Human Long Non-Coding RNAs
• Annotation of Full-Length Long Non-Coding RNAs with Capture Long-Read Sequencing (CLS)
• Single-Cell Analysis of Long Non-Coding RNAs (lncRNAs) in Mouse Brain Cells
• Detection and Characterization of Ribosome-Associated Long Non-Coding RNAs
• Analysis of Annotated and Unannotated Long Non-Coding RNAs from Exosome Subtypes Using Next-Generation RNA Sequencing
• DMS-MaPseq for Genome-Wide or Targeted RNA Structure Probing In Vitro and In Vivo
• Labeling and Purification of Temporally Expressed RNAs during the S-Phase of the Cell Cycle in Living Cells
• A Quick Immuno-FISH Protocol for Detecting RNAs, Proteins, and Chromatin Modifications
• M(R)apping RNA-Protein Interactions
• In Vivo Administration of Therapeutic Antisense Oligonucleotides
• CRISPR-Mediated Mutagenesis of Long Non-Coding RNAs
• In Vivo CRISPR/Cas9-Based Targeted Disruption and Knock-In of a Long Non-Coding RNA
• Genome-Scale Perturbation of Long Non-Coding RNA Expression Using CRISPR Interference
• In Vivo Functional Analysis of Non-Conserved Human lncRNAs Using a Humanized Mouse Model.

This detailed volume presents a comprehensive bioinformatic and experimental toolbox for prioritizing, annotating, and functionally analyzing long non-coding RNAs (lncRNAs). Playing a vital role in diverse biological progresses and human disease, lncRNAs have proven to be a challenging subject of study due to our limited understanding of their sequence-function relationships, lack of complete genetic annotation, and the unavailability of systems required to define their functional importance and molecular mechanisms, all of which this book seeks to address. 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, Functional Analysis of Long Non-Coding RNAs: Methods and Protocols provides a timely and convenient resource to facilitate the identification and characterization of disease-associated human lncRNAs, which aims to shed light on their role in biology and pathophysiology and ultimately lead toward novel therapeutic approaches targeting lncRNAs for the amelioration of human diseases.

• Preface... Table of Contents... Contributing Authors...
• 1 Detection of DNA Double Strand Breaks by -H2AX Immunodetection Sonia I. Barroso and Andres Aguilera
• 2 END-seq: An Unbiased, High-Resolution and Genome-Wide Approach to Map DNA Double Strand Breaks and Re
• section in Human Cells Nancy Wong, Sam John, Andre Nussenzweig, and Andres Canela
• 3 Resection of a DNA Double-Strand Break by Alkaline Gel Electrophoresis and Southern Blotting Erika Casari, Elisa Gobbini, Michela Clerici, and Maria Pia Longhese
• 4 Analysis of DNA Double-Strand Break Ends Resection and Single-Strand Annealing in S. pombe Zhenxin Yan, Sandeep Kumar, and Grzegorz Ira
• 5 Quantifying DNA End Re
• section in Human Cells Yi Zhou and Tanya T. Paull
• 6 Genetic and Molecular approaches to Study Chromosomal Breakage at Secondary Structure-Forming Repeats Anissia Ait Saada, Alex Costa, and Kirill S. Lobachev
• 7 Biochemical analysis of D-Loop Extension and DNA Strand Displacement Synthesis Youngho Kwon and Patrick Sung
• 8 DNA Strand Exchange to Monitor Human RAD51-Mediated Strand Invasion and Pairing Sudipta Lahiri and Ryan B. Jensen
• 9 Monitoring Homologous Recombination Activity in Human Cells Domagoj Vugic, Asa Ehlen, and Aura Carreira
• 10 Inter-Homolog Homologous Recombination in Mouse Embryonic Stem Cells Fabio Vanoli, Rohit Prakash, Travis White, and Maria Jasin
• 11 Branch Migration Activity of Rad54 Protein Olga M. Mazina and Alexander V. Mazin
• 12 Holliday Junction Resolution Raquel Carreira, F. Javier Aguado, Tomas Lama-Diaz, and Miguel G. Blanco
• 13 Identification and Analysis of Different Types of UFBs Simon Gemble and Mounira Amor-Gueret
• 14 Intrachromosomal Recombination in Yeast Anastasiya Epshtein, Lorraine S. Symington, and Hannah L. Klein
• 15 Genome-Wide Analysis of Mitotic Recombination in Budding Yeast Lydia R. Heasley, Nadia M. V. Sampaio, and Juan Lucas Argueso
• 16 Monitoring Gene Conversion in Budding Yeast by Southern Blot Analysis Miyuki Yamaguchi and James E. Haber
• 17 DNA Double-Strand Break Induced Gene Amplification in Yeast Tomas Strucko, Michael Lisby, and Uffe Hasbro Mortensen
• 18 Measuring Chromosome Pairing during Homologous Recombination in Yeast Fraulin Joseph, So Jung Lee, Eric Bryant, and Rodney Rothstein
• 19 Cytological Monitoring of Meiotic Crossovers in Spermatocytes and Oocytes Yan Yun, Masaru Ito, Sumit Sandhu, and Neil Hunter
• 20 Detection of DSBs in C. elegans Meiosis Tatiana Garcia-Muse
• 21 Methods to Map Meiotic Recombination Proteins in Saccharomyces cerevisiae Aurore Sanchez and Valerie Borde
• 22 Investigation of Break-Induced Replication in Yeast Beth Osia, Rajula Elango, Juraj Kramara, Steven A. Roberts, and Anna Malkova
• 23 Measurement of Homologous Recombination at Stalled Mammalian Replication Forks Nicholas A. Willis and Ralph Scully
• 24 Super Resolution Imaging of Homologous Recombination Repair at Collapsed Replication Forks Donna R. Whelan and Eli Rothenberg
• 25 The Analysis of Recombination-Dependent Processing of Blocked Replication Forks by Bi-Dimensional Gel Electrophoresis Karol Kramarz, Anissia Ait Saada and Sarah A.E. Lambert
• 26 The Sister Chromatid Exchange Assay in Human Cells Emanuela Tumini and Andres Aguilera
• 27 Analysis of Recombination at Yeast Telomeres Marie-Noelle Simon, Dmitri Churikov and Vincent Geli
• 28 Gel Electrophoresis Analysis of rDNA Instability in Saccharomyces cerevisiae Mariko Sasaki and Takehiko Kobayashi
• 29 Analyzing Homologous Recombination at a Genome Wide Level Coline Arnould, Vincent Rocher, and Gaelle Legube
• 30 CRISPR/Cas9 Induced Breaks in Heterochromatin, Visualized by Immunofluorescence Mitrentsi Ioanna and Evi Soutoglou
• 31 In Vivo Binding of Recombination Proteins of Non-DSB DNA Lesions to Replication Forks Roman Gonzalez-Prieto, Maria J. Cabello-Lobato and Felix Prado
• 32 Live Cell Imaging of Nuclear Actin Filaments and Heterochromatic Repair foci in Drosophila and Mouse Cells Colby See, Deepak Arya, Emily Lin, and Irene Chiolo
• 33 In Vitro Characterization of Sumoylation of HR Proteins Veronika Altmannova and Lumir Krejci
• 34 High-Throughput Analysis of Heteroduplex DNA in Mitotic Recombination Products Dionna Gamble, Yee Fang Hum, and Sue Jinks-Robertson
• 35 Fluorescence Microscopy for Analysis of Relocalization of Structure-Specific Endonucleases Carl P. Lehmann, Irene Saugar, and Jose Antonio Tercero
• 36 Physical and Genetic Assays for the Study of DNA Joint Molecules Metabolism and Multi-Invasion-Induced Rearrangements in S. cerevisiae Aurele Piazza, Pallavi Rajput, and Wolf-Dietrich Heyer.
• (source: Nielsen Book Data)

This volume explores homologous recombination's (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. .
(source: Nielsen Book Data)